** Mx startup successful ** **MX-PC 1.54** Job started on 03/04/03 at 14:36:00 !QTL analysis via Pihat method !Using marker1 !Using MZ and DZ twins !Analysis of LDL !Dutch Adults #repeat 54 Note: beginning of #Repeat section The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NSIB 2 !NUMBER OF SIBLINGS #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1284 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 183 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF1 Note: Opening #include file 1 seldef1 SELECT IBD0M1 IBD1M1 IBD2M1 LDL1 LDL2; DEFINITION IBD0M1 IBD1M1 IBD2M1; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY1 Note: Opening #include file 1 specify1 SPECIFY K IBD0M1 IBD1M1 IBD2M1 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 91.000 92.000 Mean 3.688 3.719 Variance 0.964 0.749 Minimum 1.660 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M1 IBD1M1 IBD0M1 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.501 0.240 3.558 3.632 Variance 0.047 0.020 0.032 1.012 1.164 Minimum 0.027 0.275 0.035 0.000 0.000 Maximum 0.659 0.722 0.697 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.818 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.195 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.807 0.000 0.000 0.193 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.818 0.000 0.000 0.195 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.013 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.904 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.442 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.818 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.195 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.807 0.000 0.000 0.193 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.818 0.000 0.000 0.195 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.013 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.904 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.442 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.818 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.195 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.325 2 0.574 3 0.101 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.388 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.807 0.000 0.000 0.193 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.818 0.000 0.000 0.195 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.013 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.904 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.442 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 417 Observed statistics -2 times log-likelihood of data >>> 1072.153 Degrees of freedom >>>>>>>>>>>>>>>> 412 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.03 Execution 0: 0: 0:-0.03 TOTAL 0: 0: 0: 2.00 Total number of warnings issued: 2 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 91.000 92.000 Mean 3.688 3.719 Variance 0.964 0.749 Minimum 1.660 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M1 IBD1M1 IBD0M1 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.501 0.240 3.558 3.632 Variance 0.047 0.020 0.032 1.012 1.164 Minimum 0.027 0.275 0.035 0.000 0.000 Maximum 0.659 0.722 0.697 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.818 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.195 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.807 0.000 0.000 0.193 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.818 0.000 0.000 0.195 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.013 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.904 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.442 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.818 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.195 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.807 0.000 0.000 0.193 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.818 0.000 0.000 0.195 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.013 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.904 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.442 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.818 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.195 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.325 2 0.574 3 0.101 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.388 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.807 0.000 0.000 0.193 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.818 0.000 0.000 0.195 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.013 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.904 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.442 Your model has 4 estimated parameters and 417 Observed statistics -2 times log-likelihood of data >>> 1072.153 Degrees of freedom >>>>>>>>>>>>>>>> 413 Saturated model fit* >>>>>>>>>>> 1072.153 Saturated model df* >>>>>>>>>>> 412 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.55 TOTAL 0: 0: 0: 0.55 Total number of warnings issued: 2 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF2 Note: Opening #include file 1 seldef2 SELECT IBD0M2 IBD1M2 IBD2M2 LDL1 LDL2; DEFINITION IBD0M2 IBD1M2 IBD2M2; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY2 Note: Opening #include file 1 specify2 SPECIFY K IBD0M2 IBD1M2 IBD2M2 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M2 IBD1M2 IBD0M2 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.260 0.501 0.239 3.558 3.632 Variance 0.057 0.028 0.038 1.012 1.164 Minimum 0.019 0.236 0.026 0.000 0.000 Maximum 0.702 0.761 0.745 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.328 2 0.587 3 0.085 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.378 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.19 Execution 0: 0: 0:-0.40 TOTAL 0: 0: 0: 1.79 Total number of warnings issued: 4 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M2 IBD1M2 IBD0M2 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.260 0.501 0.239 3.558 3.632 Variance 0.057 0.028 0.038 1.012 1.164 Minimum 0.019 0.236 0.026 0.000 0.000 Maximum 0.702 0.761 0.745 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.328 2 0.587 3 0.085 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.378 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.01 Execution 0: 0: 0: 0.12 TOTAL 0: 0: 0: 0.13 Total number of warnings issued: 4 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF3 Note: Opening #include file 1 seldef3 SELECT IBD0M3 IBD1M3 IBD2M3 LDL1 LDL2; DEFINITION IBD0M3 IBD1M3 IBD2M3; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY3 Note: Opening #include file 1 specify3 SPECIFY K IBD0M3 IBD1M3 IBD2M3 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M3 IBD1M3 IBD0M3 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.261 0.501 0.238 3.558 3.632 Variance 0.069 0.038 0.045 1.012 1.164 Minimum 0.011 0.191 0.018 0.000 0.000 Maximum 0.750 0.806 0.798 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.331 2 0.602 3 0.067 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.368 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.89 Execution 0: 0: 0:-0.59 TOTAL 0: 0: 0: 1.30 Total number of warnings issued: 6 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M3 IBD1M3 IBD0M3 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.261 0.501 0.238 3.558 3.632 Variance 0.069 0.038 0.045 1.012 1.164 Minimum 0.011 0.191 0.018 0.000 0.000 Maximum 0.750 0.806 0.798 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.331 2 0.602 3 0.067 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.368 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.14 TOTAL 0: 0: 0: 0.14 Total number of warnings issued: 6 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF4 Note: Opening #include file 1 seldef4 SELECT IBD0M4 IBD1M4 IBD2M4 LDL1 LDL2; DEFINITION IBD0M4 IBD1M4 IBD2M4; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY4 Note: Opening #include file 1 specify4 SPECIFY K IBD0M4 IBD1M4 IBD2M4 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M4 IBD1M4 IBD0M4 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.262 0.501 0.237 3.558 3.632 Variance 0.084 0.053 0.054 1.012 1.164 Minimum 0.005 0.137 0.011 0.000 0.000 Maximum 0.804 0.859 0.858 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.333 2 0.620 3 0.047 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.357 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.98 Execution 0: 0: 0:-0.67 TOTAL 0: 0: 0: 1.31 Total number of warnings issued: 6 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M4 IBD1M4 IBD0M4 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.262 0.501 0.237 3.558 3.632 Variance 0.084 0.053 0.054 1.012 1.164 Minimum 0.005 0.137 0.011 0.000 0.000 Maximum 0.804 0.859 0.858 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.333 2 0.620 3 0.047 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.357 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.13 TOTAL 0: 0: 0: 0.13 Total number of warnings issued: 6 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF5 Note: Opening #include file 1 seldef5 SELECT IBD0M5 IBD1M5 IBD2M5 LDL1 LDL2; DEFINITION IBD0M5 IBD1M5 IBD2M5; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY5 Note: Opening #include file 1 specify5 SPECIFY K IBD0M5 IBD1M5 IBD2M5 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M5 IBD1M5 IBD0M5 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.263 0.501 0.236 3.558 3.632 Variance 0.103 0.073 0.064 1.012 1.164 Minimum 0.001 0.074 0.005 0.000 0.000 Maximum 0.864 0.922 0.925 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.335 2 0.640 3 0.025 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.345 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.40 Execution 0: 0: 0:-1.11 TOTAL 0: 0: 0: 1.29 Total number of warnings issued: 6 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M5 IBD1M5 IBD0M5 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.263 0.501 0.236 3.558 3.632 Variance 0.103 0.073 0.064 1.012 1.164 Minimum 0.001 0.074 0.005 0.000 0.000 Maximum 0.864 0.922 0.925 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.335 2 0.640 3 0.025 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.345 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.14 TOTAL 0: 0: 0: 0.14 Total number of warnings issued: 6 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF6 Note: Opening #include file 1 seldef6 SELECT IBD0M6 IBD1M6 IBD2M6 LDL1 LDL2; DEFINITION IBD0M6 IBD1M6 IBD2M6; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY6 Note: Opening #include file 1 specify6 SPECIFY K IBD0M6 IBD1M6 IBD2M6 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M6 IBD1M6 IBD0M6 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.264 0.501 0.235 3.558 3.632 Variance 0.127 0.100 0.077 1.012 1.164 Minimum 0.000 0.000 0.001 0.000 0.000 Maximum 0.932 0.995 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.335 2 0.665 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.332 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.93 Execution 0: 0: 0:-0.27 TOTAL 0: 0: 0: 1.66 Total number of warnings issued: 6 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M6 IBD1M6 IBD0M6 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.264 0.501 0.235 3.558 3.632 Variance 0.127 0.100 0.077 1.012 1.164 Minimum 0.000 0.000 0.001 0.000 0.000 Maximum 0.932 0.995 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.335 2 0.665 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.332 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.15 TOTAL 0: 0: 0: 0.15 Total number of warnings issued: 6 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF7 Note: Opening #include file 1 seldef7 SELECT IBD0M7 IBD1M7 IBD2M7 LDL1 LDL2; DEFINITION IBD0M7 IBD1M7 IBD2M7; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY7 Note: Opening #include file 1 specify7 SPECIFY K IBD0M7 IBD1M7 IBD2M7 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M7 IBD1M7 IBD0M7 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.264 0.499 0.238 3.558 3.632 Variance 0.114 0.081 0.069 1.012 1.164 Minimum 0.000 0.028 0.001 0.000 0.000 Maximum 0.925 0.945 0.972 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.365 2 0.628 3 0.007 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.321 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.92 Execution 0: 0: 0:-0.64 TOTAL 0: 0: 0: 1.28 Total number of warnings issued: 6 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M7 IBD1M7 IBD0M7 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.264 0.499 0.238 3.558 3.632 Variance 0.114 0.081 0.069 1.012 1.164 Minimum 0.000 0.028 0.001 0.000 0.000 Maximum 0.925 0.945 0.972 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.365 2 0.628 3 0.007 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.321 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.13 TOTAL 0: 0: 0: 0.13 Total number of warnings issued: 6 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF8 Note: Opening #include file 1 seldef8 SELECT IBD0M8 IBD1M8 IBD2M8 LDL1 LDL2; DEFINITION IBD0M8 IBD1M8 IBD2M8; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY8 Note: Opening #include file 1 specify8 SPECIFY K IBD0M8 IBD1M8 IBD2M8 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M8 IBD1M8 IBD0M8 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.263 0.495 0.241 3.558 3.632 Variance 0.107 0.071 0.067 1.012 1.164 Minimum 0.000 0.050 0.002 0.000 0.000 Maximum 0.924 0.920 0.950 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.392 2 0.596 3 0.011 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.309 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.92 Execution 0: 0: 0:-0.55 TOTAL 0: 0: 0: 1.37 Total number of warnings issued: 8 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M8 IBD1M8 IBD0M8 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.263 0.495 0.241 3.558 3.632 Variance 0.107 0.071 0.067 1.012 1.164 Minimum 0.000 0.050 0.002 0.000 0.000 Maximum 0.924 0.920 0.950 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.392 2 0.596 3 0.011 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.309 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.14 TOTAL 0: 0: 0: 0.14 Total number of warnings issued: 8 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF9 Note: Opening #include file 1 seldef9 SELECT IBD0M9 IBD1M9 IBD2M9 LDL1 LDL2; DEFINITION IBD0M9 IBD1M9 IBD2M9; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY9 Note: Opening #include file 1 specify9 SPECIFY K IBD0M9 IBD1M9 IBD2M9 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M9 IBD1M9 IBD0M9 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.264 0.491 0.245 3.558 3.632 Variance 0.107 0.070 0.069 1.012 1.164 Minimum 0.001 0.066 0.001 0.000 0.000 Maximum 0.932 0.906 0.934 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.419 2 0.569 3 0.011 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.296 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.99 Execution 0: 0: 0:-0.66 TOTAL 0: 0: 0: 1.33 Total number of warnings issued: 8 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M9 IBD1M9 IBD0M9 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.264 0.491 0.245 3.558 3.632 Variance 0.107 0.070 0.069 1.012 1.164 Minimum 0.001 0.066 0.001 0.000 0.000 Maximum 0.932 0.906 0.934 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.419 2 0.569 3 0.011 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.296 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.23 TOTAL 0: 0: 0: 0.23 Total number of warnings issued: 8 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF10 Note: Opening #include file 1 seldef10 SELECT IBD0M10 IBD1M10 IBD2M10 LDL1 LDL2; DEFINITION IBD0M10 IBD1M10 IBD2M10; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY10 Note: Opening #include file 1 specify10 SPECIFY K IBD0M10 IBD1M10 IBD2M10 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M10 IBD1M10 IBD0M10 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.265 0.487 0.249 3.558 3.632 Variance 0.112 0.076 0.075 1.012 1.164 Minimum 0.001 0.054 0.001 0.000 0.000 Maximum 0.946 0.907 0.923 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.446 2 0.545 3 0.009 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.281 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.01 Execution 0: 0: 0:-0.59 TOTAL 0: 0: 0: 1.42 Total number of warnings issued: 8 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M10 IBD1M10 IBD0M10 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.265 0.487 0.249 3.558 3.632 Variance 0.112 0.076 0.075 1.012 1.164 Minimum 0.001 0.054 0.001 0.000 0.000 Maximum 0.946 0.907 0.923 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.446 2 0.545 3 0.009 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.281 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.01 Execution 0: 0: 0: 0.12 TOTAL 0: 0: 0: 0.13 Total number of warnings issued: 8 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF11 Note: Opening #include file 1 seldef11 SELECT IBD0M11 IBD1M11 IBD2M11 LDL1 LDL2; DEFINITION IBD0M11 IBD1M11 IBD2M11; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY11 Note: Opening #include file 1 specify11 SPECIFY K IBD0M11 IBD1M11 IBD2M11 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M11 IBD1M11 IBD0M11 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.266 0.481 0.253 3.558 3.632 Variance 0.124 0.090 0.086 1.012 1.164 Minimum 0.000 0.029 0.000 0.000 0.000 Maximum 0.965 0.941 0.971 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.472 2 0.524 3 0.003 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.265 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.53 Execution 0: 0: 0:-0.98 TOTAL 0: 0: 0: 1.55 Total number of warnings issued: 10 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M11 IBD1M11 IBD0M11 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.266 0.481 0.253 3.558 3.632 Variance 0.124 0.090 0.086 1.012 1.164 Minimum 0.000 0.029 0.000 0.000 0.000 Maximum 0.965 0.941 0.971 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.472 2 0.524 3 0.003 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.265 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.13 TOTAL 0: 0: 0: 0.13 Total number of warnings issued: 10 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF12 Note: Opening #include file 1 seldef12 SELECT IBD0M12 IBD1M12 IBD2M12 LDL1 LDL2; DEFINITION IBD0M12 IBD1M12 IBD2M12; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY12 Note: Opening #include file 1 specify12 SPECIFY K IBD0M12 IBD1M12 IBD2M12 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M12 IBD1M12 IBD0M12 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.262 0.483 0.255 3.558 3.632 Variance 0.126 0.095 0.091 1.012 1.164 Minimum 0.000 0.006 0.000 0.000 0.000 Maximum 0.973 0.946 0.994 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.485 2 0.511 3 0.004 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.260 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.00 Execution 0: 0: 0:-0.48 TOTAL 0: 0: 0: 1.52 Total number of warnings issued: 10 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M12 IBD1M12 IBD0M12 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.262 0.483 0.255 3.558 3.632 Variance 0.126 0.095 0.091 1.012 1.164 Minimum 0.000 0.006 0.000 0.000 0.000 Maximum 0.973 0.946 0.994 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.485 2 0.511 3 0.004 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.260 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.46 TOTAL 0: 0: 0: 0.46 Total number of warnings issued: 10 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF13 Note: Opening #include file 1 seldef13 SELECT IBD0M13 IBD1M13 IBD2M13 LDL1 LDL2; DEFINITION IBD0M13 IBD1M13 IBD2M13; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY13 Note: Opening #include file 1 specify13 SPECIFY K IBD0M13 IBD1M13 IBD2M13 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M13 IBD1M13 IBD0M13 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.253 0.493 0.254 3.558 3.632 Variance 0.121 0.097 0.092 1.012 1.164 Minimum 0.000 0.012 0.000 0.000 0.000 Maximum 0.971 0.945 0.988 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.486 2 0.504 3 0.010 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.262 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.99 Execution 0: 0: 0: 0.05 TOTAL 0: 0: 0: 2.04 Total number of warnings issued: 12 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M13 IBD1M13 IBD0M13 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.253 0.493 0.254 3.558 3.632 Variance 0.121 0.097 0.092 1.012 1.164 Minimum 0.000 0.012 0.000 0.000 0.000 Maximum 0.971 0.945 0.988 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.486 2 0.504 3 0.010 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.262 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.838 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.14 TOTAL 0: 0: 0: 0.14 Total number of warnings issued: 12 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF14 Note: Opening #include file 1 seldef14 SELECT IBD0M14 IBD1M14 IBD2M14 LDL1 LDL2; DEFINITION IBD0M14 IBD1M14 IBD2M14; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY14 Note: Opening #include file 1 specify14 SPECIFY K IBD0M14 IBD1M14 IBD2M14 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M14 IBD1M14 IBD0M14 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.243 0.503 0.254 3.558 3.632 Variance 0.125 0.113 0.102 1.012 1.164 Minimum 0.000 0.012 0.000 0.000 0.000 Maximum 0.974 0.955 0.988 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.742 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.015 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.167 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.028 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.720 0.015 0.027 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.742 0.015 0.028 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.862 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.124 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.742 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.015 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.167 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.028 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.720 0.015 0.027 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.742 0.015 0.028 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.862 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.124 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.742 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.015 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.487 2 0.499 3 0.014 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.167 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.264 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.028 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.720 0.015 0.027 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.742 0.015 0.028 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.862 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.124 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.832 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.00 Execution 0: 0: 0: 0.27 TOTAL 0: 0: 0: 2.27 Total number of warnings issued: 12 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M14 IBD1M14 IBD0M14 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.243 0.503 0.254 3.558 3.632 Variance 0.125 0.113 0.102 1.012 1.164 Minimum 0.000 0.012 0.000 0.000 0.000 Maximum 0.974 0.955 0.988 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.487 2 0.499 3 0.014 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.264 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.832 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.006 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.936 Akaike's Information Criterion > -1.994 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.80 TOTAL 0: 0: 0: 0.80 Total number of warnings issued: 12 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF15 Note: Opening #include file 1 seldef15 SELECT IBD0M15 IBD1M15 IBD2M15 LDL1 LDL2; DEFINITION IBD0M15 IBD1M15 IBD2M15; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY15 Note: Opening #include file 1 specify15 SPECIFY K IBD0M15 IBD1M15 IBD2M15 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M15 IBD1M15 IBD0M15 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.233 0.514 0.253 3.558 3.632 Variance 0.137 0.144 0.120 1.012 1.164 Minimum 0.000 0.006 0.000 0.000 0.000 Maximum 0.986 0.977 0.994 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.593 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.005 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.432 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.187 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.576 0.005 0.181 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.593 0.005 0.187 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.029 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.770 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.069 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.593 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.005 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.432 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.187 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.576 0.005 0.181 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.593 0.005 0.187 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.029 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.770 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.069 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.593 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.005 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.488 2 0.497 3 0.015 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.432 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.263 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.187 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.576 0.005 0.181 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.593 0.005 0.187 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.029 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.770 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.069 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.491 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 6.76 Execution 0: 0: 0:-4.60 TOTAL 0: 0: 0: 2.16 Total number of warnings issued: 12 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M15 IBD1M15 IBD0M15 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.233 0.514 0.253 3.558 3.632 Variance 0.137 0.144 0.120 1.012 1.164 Minimum 0.000 0.006 0.000 0.000 0.000 Maximum 0.986 0.977 0.994 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.488 2 0.497 3 0.015 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.263 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.491 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.347 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.556 Akaike's Information Criterion > -1.653 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.90 TOTAL 0: 0: 0: 0.90 Total number of warnings issued: 12 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF16 Note: Opening #include file 1 seldef16 SELECT IBD0M16 IBD1M16 IBD2M16 LDL1 LDL2; DEFINITION IBD0M16 IBD1M16 IBD2M16; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY16 Note: Opening #include file 1 specify16 SPECIFY K IBD0M16 IBD1M16 IBD2M16 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M16 IBD1M16 IBD0M16 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.226 0.517 0.257 3.558 3.632 Variance 0.138 0.161 0.134 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.996 0.998 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.511 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.002 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.520 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.271 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.497 0.002 0.263 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.511 0.002 0.271 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.029 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.715 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.045 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.511 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.002 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.520 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.271 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.497 0.002 0.263 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.511 0.002 0.271 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.029 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.715 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.045 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.511 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.002 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.491 2 0.497 3 0.013 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.520 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.261 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.271 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.497 0.002 0.263 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.511 0.002 0.271 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.029 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.715 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.045 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.959 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.01 Execution 0: 0: 0:-0.60 TOTAL 0: 0: 0: 1.41 Total number of warnings issued: 12 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M16 IBD1M16 IBD0M16 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.226 0.517 0.257 3.558 3.632 Variance 0.138 0.161 0.134 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.996 0.998 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.491 2 0.497 3 0.013 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.261 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.959 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.879 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.348 Akaike's Information Criterion > -1.121 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.88 TOTAL 0: 0: 0: 0.88 Total number of warnings issued: 12 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF17 Note: Opening #include file 1 seldef17 SELECT IBD0M17 IBD1M17 IBD2M17 LDL1 LDL2; DEFINITION IBD0M17 IBD1M17 IBD2M17; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY17 Note: Opening #include file 1 specify17 SPECIFY K IBD0M17 IBD1M17 IBD2M17 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M17 IBD1M17 IBD0M17 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.222 0.512 0.266 3.558 3.632 Variance 0.141 0.175 0.149 1.012 1.164 Minimum 0.000 0.001 0.000 0.000 0.000 Maximum 0.998 0.999 0.999 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.453 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.002 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.574 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.329 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.440 0.002 0.320 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.453 0.002 0.329 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.028 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.673 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.040 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.453 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.002 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.574 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.329 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.440 0.002 0.320 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.453 0.002 0.329 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.028 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.673 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.040 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.453 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.002 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.493 2 0.498 3 0.009 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.574 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.258 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.329 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.440 0.002 0.320 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.453 0.002 0.329 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.028 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.673 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.040 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.402 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.39 Execution 0: 0: 0:-0.06 TOTAL 0: 0: 0: 2.33 Total number of warnings issued: 14 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M17 IBD1M17 IBD0M17 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.222 0.512 0.266 3.558 3.632 Variance 0.141 0.175 0.149 1.012 1.164 Minimum 0.000 0.001 0.000 0.000 0.000 Maximum 0.998 0.999 0.999 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.493 2 0.498 3 0.009 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.258 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.402 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.437 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.231 Akaike's Information Criterion > -0.563 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.97 TOTAL 0: 0: 0: 0.97 Total number of warnings issued: 14 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF18 Note: Opening #include file 1 seldef18 SELECT IBD0M18 IBD1M18 IBD2M18 LDL1 LDL2; DEFINITION IBD0M18 IBD1M18 IBD2M18; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY18 Note: Opening #include file 1 specify18 SPECIFY K IBD0M18 IBD1M18 IBD2M18 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M18 IBD1M18 IBD0M18 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.220 0.503 0.276 3.558 3.632 Variance 0.140 0.182 0.162 1.012 1.164 Minimum 0.000 0.000 0.000 0.000 0.000 Maximum 0.998 0.998 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.358 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.650 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.423 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.349 0.000 0.412 0.239 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.358 0.000 0.423 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.027 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.599 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.496 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.358 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.650 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.423 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.349 0.000 0.412 0.239 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.358 0.000 0.423 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.027 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.599 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.496 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.358 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.496 2 0.502 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.650 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.253 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.423 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.349 0.000 0.412 0.239 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.358 0.000 0.423 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.027 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.599 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.496 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1097.273 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.89 Execution 0: 0: 0:-0.49 TOTAL 0: 0: 0: 1.40 Total number of warnings issued: 14 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M18 IBD1M18 IBD0M18 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.220 0.503 0.276 3.558 3.632 Variance 0.140 0.182 0.162 1.012 1.164 Minimum 0.000 0.000 0.000 0.000 0.000 Maximum 0.998 0.998 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.496 2 0.502 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.253 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1097.273 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 2.565 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.109 Akaike's Information Criterion > 0.565 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.14 TOTAL 0: 0: 0: 1.14 Total number of warnings issued: 16 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF19 Note: Opening #include file 1 seldef19 SELECT IBD0M19 IBD1M19 IBD2M19 LDL1 LDL2; DEFINITION IBD0M19 IBD1M19 IBD2M19; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY19 Note: Opening #include file 1 specify19 SPECIFY K IBD0M19 IBD1M19 IBD2M19 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M19 IBD1M19 IBD0M19 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.215 0.505 0.280 3.558 3.632 Variance 0.125 0.157 0.150 1.012 1.164 Minimum 0.000 0.008 0.000 0.000 0.000 Maximum 0.989 0.980 0.992 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.220 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.748 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.559 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.215 0.000 0.545 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.220 0.000 0.559 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.469 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.220 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.748 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.559 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.215 0.000 0.545 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.220 0.000 0.559 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.469 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.220 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.593 2 0.406 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.748 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.205 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.559 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.215 0.000 0.545 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.220 0.000 0.559 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.469 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1095.521 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.09 Execution 0: 0: 0:-0.37 TOTAL 0: 0: 0: 1.72 Total number of warnings issued: 18 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M19 IBD1M19 IBD0M19 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.215 0.505 0.280 3.558 3.632 Variance 0.125 0.157 0.150 1.012 1.164 Minimum 0.000 0.008 0.000 0.000 0.000 Maximum 0.989 0.980 0.992 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.593 2 0.406 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.205 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1095.521 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 4.317 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.038 Akaike's Information Criterion > 2.317 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.38 TOTAL 0: 0: 0: 1.38 Total number of warnings issued: 18 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF20 Note: Opening #include file 1 seldef20 SELECT IBD0M20 IBD1M20 IBD2M20 LDL1 LDL2; DEFINITION IBD0M20 IBD1M20 IBD2M20; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY20 Note: Opening #include file 1 specify20 SPECIFY K IBD0M20 IBD1M20 IBD2M20 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M20 IBD1M20 IBD0M20 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.208 0.509 0.282 3.558 3.632 Variance 0.109 0.134 0.137 1.012 1.164 Minimum 0.000 0.013 0.000 0.000 0.000 Maximum 0.984 0.970 0.987 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.101 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.823 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.677 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.099 0.000 0.661 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.101 0.000 0.677 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.024 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.318 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.496 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.101 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.823 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.677 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.099 0.000 0.661 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.101 0.000 0.677 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.024 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.318 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.496 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.101 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.714 2 0.284 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.823 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.144 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.677 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.099 0.000 0.661 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.101 0.000 0.677 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.024 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.318 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.496 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1093.428 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.01 Execution 0: 0: 0:-0.13 TOTAL 0: 0: 0: 1.88 Total number of warnings issued: 18 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M20 IBD1M20 IBD0M20 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.208 0.509 0.282 3.558 3.632 Variance 0.109 0.134 0.137 1.012 1.164 Minimum 0.000 0.013 0.000 0.000 0.000 Maximum 0.984 0.970 0.987 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.714 2 0.284 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.144 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1093.428 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 6.410 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.011 Akaike's Information Criterion > 4.410 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.29 TOTAL 0: 0: 0: 1.29 Total number of warnings issued: 18 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF21 Note: Opening #include file 1 seldef21 SELECT IBD0M21 IBD1M21 IBD2M21 LDL1 LDL2; DEFINITION IBD0M21 IBD1M21 IBD2M21; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY21 Note: Opening #include file 1 specify21 SPECIFY K IBD0M21 IBD1M21 IBD2M21 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M21 IBD1M21 IBD0M21 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.200 0.515 0.284 3.558 3.632 Variance 0.104 0.129 0.133 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.985 0.971 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.033 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.862 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.743 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.032 0.000 0.728 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.033 0.000 0.743 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.181 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.033 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.862 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.743 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.032 0.000 0.728 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.033 0.000 0.743 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.181 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.033 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.840 2 0.160 3 0.001 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.862 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.081 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.743 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.032 0.000 0.728 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.033 0.000 0.743 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.181 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1091.458 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.97 Execution 0: 0: 0: 0.08 TOTAL 0: 0: 0: 2.05 Total number of warnings issued: 18 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M21 IBD1M21 IBD0M21 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.200 0.515 0.284 3.558 3.632 Variance 0.104 0.129 0.133 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.985 0.971 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.840 2 0.160 3 0.001 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.081 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1091.458 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 8.380 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.004 Akaike's Information Criterion > 6.380 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.10 TOTAL 0: 0: 0: 1.10 Total number of warnings issued: 18 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF22 Note: Opening #include file 1 seldef22 SELECT IBD0M22 IBD1M22 IBD2M22 LDL1 LDL2; DEFINITION IBD0M22 IBD1M22 IBD2M22; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY22 Note: Opening #include file 1 specify22 SPECIFY K IBD0M22 IBD1M22 IBD2M22 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M22 IBD1M22 IBD0M22 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.192 0.523 0.286 3.558 3.632 Variance 0.110 0.142 0.137 1.012 1.164 Minimum 0.000 0.003 0.000 0.000 0.000 Maximum 0.992 0.985 0.997 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.010 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.244 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.875 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.765 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.010 0.750 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.010 0.765 0.244 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.020 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.101 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.494 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.010 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.244 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.875 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.765 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.010 0.750 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.010 0.765 0.244 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.020 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.101 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.494 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.010 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.244 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.970 2 0.030 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.875 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.015 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.765 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.010 0.750 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.010 0.765 0.244 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.020 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.101 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.494 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1089.801 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.03 Execution 0: 0: 0: 0.36 TOTAL 0: 0: 0: 2.39 Total number of warnings issued: 20 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M22 IBD1M22 IBD0M22 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.192 0.523 0.286 3.558 3.632 Variance 0.110 0.142 0.137 1.012 1.164 Minimum 0.000 0.003 0.000 0.000 0.000 Maximum 0.992 0.985 0.997 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.970 2 0.030 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.015 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1089.801 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 10.037 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.002 Akaike's Information Criterion > 8.037 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.43 TOTAL 0: 0: 0: 1.43 Total number of warnings issued: 20 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF23 Note: Opening #include file 1 seldef23 SELECT IBD0M23 IBD1M23 IBD2M23 LDL1 LDL2; DEFINITION IBD0M23 IBD1M23 IBD2M23; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY23 Note: Opening #include file 1 specify23 SPECIFY K IBD0M23 IBD1M23 IBD2M23 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M23 IBD1M23 IBD0M23 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.187 0.524 0.290 3.558 3.632 Variance 0.096 0.128 0.133 1.012 1.164 Minimum 0.000 0.009 0.000 0.000 0.000 Maximum 0.985 0.973 0.991 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.240 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.881 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.776 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.764 0.236 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.776 0.240 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.016 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.490 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.240 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.881 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.776 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.764 0.236 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.776 0.240 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.016 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.490 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.240 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.909 2 0.090 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.881 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.045 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.776 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.764 0.236 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.776 0.240 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.016 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.490 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1088.010 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.83 Execution 0: 0: 0: 0.57 TOTAL 0: 0: 0: 2.40 Total number of warnings issued: 22 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M23 IBD1M23 IBD0M23 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.187 0.524 0.290 3.558 3.632 Variance 0.096 0.128 0.133 1.012 1.164 Minimum 0.000 0.009 0.000 0.000 0.000 Maximum 0.985 0.973 0.991 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.909 2 0.090 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.045 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1088.010 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 11.828 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 9.828 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.30 TOTAL 0: 0: 0: 1.30 Total number of warnings issued: 22 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF24 Note: Opening #include file 1 seldef24 SELECT IBD0M24 IBD1M24 IBD2M24 LDL1 LDL2; DEFINITION IBD0M24 IBD1M24 IBD2M24; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY24 Note: Opening #include file 1 specify24 SPECIFY K IBD0M24 IBD1M24 IBD2M24 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M24 IBD1M24 IBD0M24 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.182 0.525 0.294 3.558 3.632 Variance 0.086 0.118 0.132 1.012 1.164 Minimum 0.000 0.014 0.000 0.000 0.000 Maximum 0.979 0.963 0.986 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.775 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.766 0.234 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.775 0.237 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.012 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.487 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.775 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.766 0.234 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.775 0.237 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.012 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.487 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.799 2 0.200 3 0.001 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.101 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.775 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.766 0.234 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.775 0.237 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.012 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.487 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1086.479 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.82 Execution 0: 0: 0: 0.10 TOTAL 0: 0: 0: 1.92 Total number of warnings issued: 22 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M24 IBD1M24 IBD0M24 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.182 0.525 0.294 3.558 3.632 Variance 0.086 0.118 0.132 1.012 1.164 Minimum 0.000 0.014 0.000 0.000 0.000 Maximum 0.979 0.963 0.986 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.799 2 0.200 3 0.001 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.101 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1086.479 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 13.359 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 11.359 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.25 TOTAL 0: 0: 0: 1.25 Total number of warnings issued: 22 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF25 Note: Opening #include file 1 seldef25 SELECT IBD0M25 IBD1M25 IBD2M25 LDL1 LDL2; DEFINITION IBD0M25 IBD1M25 IBD2M25; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY25 Note: Opening #include file 1 specify25 SPECIFY K IBD0M25 IBD1M25 IBD2M25 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M25 IBD1M25 IBD0M25 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.176 0.527 0.298 3.558 3.632 Variance 0.086 0.123 0.135 1.012 1.164 Minimum 0.000 0.013 0.000 0.000 0.000 Maximum 0.982 0.965 0.987 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.235 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.773 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.767 0.233 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.773 0.235 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.009 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.485 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.235 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.773 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.767 0.233 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.773 0.235 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.009 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.485 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.235 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.693 2 0.305 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.154 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.773 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.767 0.233 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.773 0.235 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.009 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.485 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1085.112 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.90 Execution 0: 0: 0: 0.17 TOTAL 0: 0: 0: 2.07 Total number of warnings issued: 22 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M25 IBD1M25 IBD0M25 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.176 0.527 0.298 3.558 3.632 Variance 0.086 0.123 0.135 1.012 1.164 Minimum 0.000 0.013 0.000 0.000 0.000 Maximum 0.982 0.965 0.987 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.693 2 0.305 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.154 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1085.112 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 14.726 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 12.726 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.47 TOTAL 0: 0: 0: 1.47 Total number of warnings issued: 22 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF26 Note: Opening #include file 1 seldef26 SELECT IBD0M26 IBD1M26 IBD2M26 LDL1 LDL2; DEFINITION IBD0M26 IBD1M26 IBD2M26; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY26 Note: Opening #include file 1 specify26 SPECIFY K IBD0M26 IBD1M26 IBD2M26 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M26 IBD1M26 IBD0M26 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.168 0.530 0.301 3.558 3.632 Variance 0.097 0.144 0.145 1.012 1.164 Minimum 0.000 0.006 0.000 0.000 0.000 Maximum 0.991 0.979 0.994 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.234 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.773 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.768 0.232 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.773 0.234 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.484 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.234 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.773 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.768 0.232 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.773 0.234 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.484 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.234 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.590 2 0.409 3 0.001 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.205 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.773 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.768 0.232 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.773 0.234 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.484 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1083.763 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.09 Execution 0: 0: 0:-0.27 TOTAL 0: 0: 0: 1.82 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M26 IBD1M26 IBD0M26 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.168 0.530 0.301 3.558 3.632 Variance 0.097 0.144 0.145 1.012 1.164 Minimum 0.000 0.006 0.000 0.000 0.000 Maximum 0.991 0.979 0.994 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.590 2 0.409 3 0.001 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.205 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1083.763 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 16.075 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 14.075 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.19 TOTAL 0: 0: 0: 1.19 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF27 Note: Opening #include file 1 seldef27 SELECT IBD0M27 IBD1M27 IBD2M27 LDL1 LDL2; DEFINITION IBD0M27 IBD1M27 IBD2M27; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY27 Note: Opening #include file 1 specify27 SPECIFY K IBD0M27 IBD1M27 IBD2M27 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M27 IBD1M27 IBD0M27 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.157 0.539 0.304 3.558 3.632 Variance 0.108 0.165 0.150 1.012 1.164 Minimum 0.000 0.000 0.000 0.000 0.000 Maximum 0.997 0.997 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.234 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.768 0.232 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.234 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.008 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.484 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.234 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.768 0.232 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.234 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.008 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.484 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.234 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.555 2 0.445 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.223 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.768 0.232 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.234 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.008 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.484 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1084.097 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.90 Execution 0: 0: 0:-0.13 TOTAL 0: 0: 0: 1.77 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M27 IBD1M27 IBD0M27 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.157 0.539 0.304 3.558 3.632 Variance 0.108 0.165 0.150 1.012 1.164 Minimum 0.000 0.000 0.000 0.000 0.000 Maximum 0.997 0.997 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.555 2 0.445 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.223 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1084.097 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 15.741 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 13.741 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.29 TOTAL 0: 0: 0: 1.29 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF28 Note: Opening #include file 1 seldef28 SELECT IBD0M28 IBD1M28 IBD2M28 LDL1 LDL2; DEFINITION IBD0M28 IBD1M28 IBD2M28; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY28 Note: Opening #include file 1 specify28 SPECIFY K IBD0M28 IBD1M28 IBD2M28 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M28 IBD1M28 IBD0M28 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.161 0.538 0.301 3.558 3.632 Variance 0.090 0.129 0.130 1.012 1.164 Minimum 0.000 0.014 0.000 0.000 0.000 Maximum 0.980 0.967 0.986 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.235 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.772 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.767 0.233 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.772 0.235 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.485 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.235 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.772 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.767 0.233 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.772 0.235 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.485 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.235 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.600 2 0.397 3 0.004 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.202 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.772 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.767 0.233 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.772 0.235 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.485 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1085.124 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.85 Execution 0: 0: 0:-0.10 TOTAL 0: 0: 0: 1.75 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M28 IBD1M28 IBD0M28 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.161 0.538 0.301 3.558 3.632 Variance 0.090 0.129 0.130 1.012 1.164 Minimum 0.000 0.014 0.000 0.000 0.000 Maximum 0.980 0.967 0.986 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.600 2 0.397 3 0.004 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.202 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1085.124 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 14.714 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 12.714 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.43 TOTAL 0: 0: 0: 1.43 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF29 Note: Opening #include file 1 seldef29 SELECT IBD0M29 IBD1M29 IBD2M29 LDL1 LDL2; DEFINITION IBD0M29 IBD1M29 IBD2M29; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY29 Note: Opening #include file 1 specify29 SPECIFY K IBD0M29 IBD1M29 IBD2M29 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M29 IBD1M29 IBD0M29 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.165 0.537 0.298 3.558 3.632 Variance 0.080 0.110 0.120 1.012 1.164 Minimum 0.000 0.022 0.000 0.000 0.000 Maximum 0.969 0.952 0.978 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.236 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.771 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.766 0.234 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.771 0.236 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.486 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.236 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.771 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.766 0.234 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.771 0.236 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.486 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.236 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.647 2 0.348 3 0.005 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.179 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.771 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.766 0.234 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.771 0.236 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.007 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.486 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1085.991 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.82 Execution 0: 0: 0: 0.06 TOTAL 0: 0: 0: 1.88 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M29 IBD1M29 IBD0M29 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.165 0.537 0.298 3.558 3.632 Variance 0.080 0.110 0.120 1.012 1.164 Minimum 0.000 0.022 0.000 0.000 0.000 Maximum 0.969 0.952 0.978 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.647 2 0.348 3 0.005 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.179 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1085.991 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 13.847 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 11.847 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.26 TOTAL 0: 0: 0: 1.26 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF30 Note: Opening #include file 1 seldef30 SELECT IBD0M30 IBD1M30 IBD2M30 LDL1 LDL2; DEFINITION IBD0M30 IBD1M30 IBD2M30; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY30 Note: Opening #include file 1 specify30 SPECIFY K IBD0M30 IBD1M30 IBD2M30 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M30 IBD1M30 IBD0M30 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.168 0.536 0.296 3.558 3.632 Variance 0.077 0.105 0.117 1.012 1.164 Minimum 0.000 0.024 0.000 0.000 0.000 Maximum 0.965 0.948 0.976 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.771 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.765 0.235 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.771 0.237 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.008 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.487 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.771 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.765 0.235 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.771 0.237 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.008 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.487 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.237 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.696 2 0.299 3 0.005 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.155 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.771 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.765 0.235 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.771 0.237 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.008 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.487 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1086.771 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.07 Execution 0: 0: 0:-0.13 TOTAL 0: 0: 0: 1.94 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M30 IBD1M30 IBD0M30 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.168 0.536 0.296 3.558 3.632 Variance 0.077 0.105 0.117 1.012 1.164 Minimum 0.000 0.024 0.000 0.000 0.000 Maximum 0.965 0.948 0.976 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.696 2 0.299 3 0.005 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.155 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1086.771 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 13.068 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 11.068 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.32 TOTAL 0: 0: 0: 1.32 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF31 Note: Opening #include file 1 seldef31 SELECT IBD0M31 IBD1M31 IBD2M31 LDL1 LDL2; DEFINITION IBD0M31 IBD1M31 IBD2M31; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY31 Note: Opening #include file 1 specify31 SPECIFY K IBD0M31 IBD1M31 IBD2M31 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M31 IBD1M31 IBD0M31 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.170 0.536 0.294 3.558 3.632 Variance 0.082 0.113 0.122 1.012 1.164 Minimum 0.000 0.020 0.000 0.000 0.000 Maximum 0.968 0.955 0.980 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.238 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.772 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.764 0.236 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.772 0.238 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.010 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.488 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.238 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.772 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.764 0.236 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.772 0.238 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.010 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.488 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.238 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.748 2 0.248 3 0.004 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.879 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.128 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.772 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.764 0.236 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.772 0.238 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.010 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.488 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1087.503 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.01 Execution 0: 0: 0:-0.13 TOTAL 0: 0: 0: 1.88 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M31 IBD1M31 IBD0M31 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.170 0.536 0.294 3.558 3.632 Variance 0.082 0.113 0.122 1.012 1.164 Minimum 0.000 0.020 0.000 0.000 0.000 Maximum 0.968 0.955 0.980 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.748 2 0.248 3 0.004 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.128 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1087.503 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 12.335 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 10.335 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.01 Execution 0: 0: 0: 1.20 TOTAL 0: 0: 0: 1.21 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF32 Note: Opening #include file 1 seldef32 SELECT IBD0M32 IBD1M32 IBD2M32 LDL1 LDL2; DEFINITION IBD0M32 IBD1M32 IBD2M32; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY32 Note: Opening #include file 1 specify32 SPECIFY K IBD0M32 IBD1M32 IBD2M32 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M32 IBD1M32 IBD0M32 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.172 0.535 0.292 3.558 3.632 Variance 0.095 0.135 0.134 1.012 1.164 Minimum 0.000 0.010 0.000 0.000 0.000 Maximum 0.978 0.974 0.990 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.240 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.636 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.763 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.240 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.014 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.490 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.240 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.636 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.763 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.240 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.014 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.490 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.240 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.804 2 0.194 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.636 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.099 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.763 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.240 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.014 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.490 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1088.237 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.82 Execution 0: 0: 0:-0.08 TOTAL 0: 0: 0: 1.74 Total number of warnings issued: 24 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M32 IBD1M32 IBD0M32 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.172 0.535 0.292 3.558 3.632 Variance 0.095 0.135 0.134 1.012 1.164 Minimum 0.000 0.010 0.000 0.000 0.000 Maximum 0.978 0.974 0.990 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.804 2 0.194 3 0.002 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.099 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1088.237 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 11.601 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 9.601 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.28 TOTAL 0: 0: 0: 1.28 Total number of warnings issued: 24 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF33 Note: Opening #include file 1 seldef33 SELECT IBD0M33 IBD1M33 IBD2M33 LDL1 LDL2; DEFINITION IBD0M33 IBD1M33 IBD2M33; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY33 Note: Opening #include file 1 specify33 SPECIFY K IBD0M33 IBD1M33 IBD2M33 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M33 IBD1M33 IBD0M33 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.178 0.531 0.290 3.558 3.632 Variance 0.108 0.156 0.148 1.012 1.164 Minimum 0.000 0.001 0.000 0.000 0.000 Maximum 0.990 0.992 0.999 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.242 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.636 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.762 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.242 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.016 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.492 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.242 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.636 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.762 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.242 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.016 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.492 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.242 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.871 2 0.129 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.880 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.636 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.065 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.774 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.762 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.774 0.242 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.016 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.492 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1088.731 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.82 Execution 0: 0: 0: 0.13 TOTAL 0: 0: 0: 1.95 Total number of warnings issued: 26 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M33 IBD1M33 IBD0M33 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.178 0.531 0.290 3.558 3.632 Variance 0.108 0.156 0.148 1.012 1.164 Minimum 0.000 0.001 0.000 0.000 0.000 Maximum 0.990 0.992 0.999 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.871 2 0.129 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.065 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1088.731 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 11.107 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 9.107 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.29 TOTAL 0: 0: 0: 1.29 Total number of warnings issued: 26 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF34 Note: Opening #include file 1 seldef34 SELECT IBD0M34 IBD1M34 IBD2M34 LDL1 LDL2; DEFINITION IBD0M34 IBD1M34 IBD2M34; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY34 Note: Opening #include file 1 specify34 SPECIFY K IBD0M34 IBD1M34 IBD2M34 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M34 IBD1M34 IBD0M34 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.191 0.521 0.288 3.558 3.632 Variance 0.122 0.171 0.156 1.012 1.164 Minimum 0.000 0.001 0.000 0.000 0.000 Maximum 0.997 0.997 0.999 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.637 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.770 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.757 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.770 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.018 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.497 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.637 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.770 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.757 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.770 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.018 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.497 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.000 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.953 2 0.047 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.878 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.637 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.024 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.770 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.000 0.000 0.757 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.000 0.000 0.770 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.018 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.497 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1089.523 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.22 Execution 0: 0: 0:-0.68 TOTAL 0: 0: 0: 1.54 Total number of warnings issued: 28 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M34 IBD1M34 IBD0M34 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.191 0.521 0.288 3.558 3.632 Variance 0.122 0.171 0.156 1.012 1.164 Minimum 0.000 0.001 0.000 0.000 0.000 Maximum 0.997 0.997 0.999 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.953 2 0.047 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.024 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1089.523 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 10.315 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.001 Akaike's Information Criterion > 8.315 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.23 TOTAL 0: 0: 0: 1.23 Total number of warnings issued: 28 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF35 Note: Opening #include file 1 seldef35 SELECT IBD0M35 IBD1M35 IBD2M35 LDL1 LDL2; DEFINITION IBD0M35 IBD1M35 IBD2M35; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY35 Note: Opening #include file 1 specify35 SPECIFY K IBD0M35 IBD1M35 IBD2M35 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M35 IBD1M35 IBD0M35 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.217 0.498 0.286 3.558 3.632 Variance 0.136 0.176 0.161 1.012 1.164 Minimum 0.000 0.000 0.000 0.000 0.000 Maximum 1.000 1.000 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.144 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.250 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.792 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.627 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.141 0.000 0.614 0.245 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.144 0.000 0.627 0.250 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.379 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.500 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.144 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.250 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.792 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.627 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.141 0.000 0.614 0.245 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.144 0.000 0.627 0.250 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.379 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.500 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.144 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.250 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.996 2 0.004 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.792 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.002 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.627 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.141 0.000 0.614 0.245 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.144 0.000 0.627 0.250 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.379 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.500 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1093.579 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.82 Execution 0: 0: 0:-0.36 TOTAL 0: 0: 0: 1.46 Total number of warnings issued: 30 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M35 IBD1M35 IBD0M35 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.217 0.498 0.286 3.558 3.632 Variance 0.136 0.176 0.161 1.012 1.164 Minimum 0.000 0.000 0.000 0.000 0.000 Maximum 1.000 1.000 1.000 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.996 2 0.004 3 0.000 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.002 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1093.579 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 6.259 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.012 Akaike's Information Criterion > 4.259 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.68 TOTAL 0: 0: 0: 1.68 Total number of warnings issued: 30 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF36 Note: Opening #include file 1 seldef36 SELECT IBD0M36 IBD1M36 IBD2M36 LDL1 LDL2; DEFINITION IBD0M36 IBD1M36 IBD2M36; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY36 Note: Opening #include file 1 specify36 SPECIFY K IBD0M36 IBD1M36 IBD2M36 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M36 IBD1M36 IBD0M36 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.221 0.500 0.279 3.558 3.632 Variance 0.147 0.177 0.152 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.996 0.994 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.323 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.248 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.670 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.449 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.317 0.000 0.440 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.323 0.000 0.449 0.248 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.569 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.498 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.323 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.248 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.670 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.449 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.317 0.000 0.440 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.323 0.000 0.449 0.248 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.569 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.498 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.323 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.248 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.274 2 0.703 3 0.023 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.670 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.375 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.449 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.317 0.000 0.440 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.323 0.000 0.449 0.248 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.021 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.569 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.498 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1096.200 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 3.38 Execution 0: 0: 0:-1.19 TOTAL 0: 0: 0: 2.19 Total number of warnings issued: 32 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M36 IBD1M36 IBD0M36 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.221 0.500 0.279 3.558 3.632 Variance 0.147 0.177 0.152 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.996 0.994 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.274 2 0.703 3 0.023 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.375 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1096.200 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 3.639 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.056 Akaike's Information Criterion > 1.639 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.51 TOTAL 0: 0: 0: 1.51 Total number of warnings issued: 32 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF37 Note: Opening #include file 1 seldef37 SELECT IBD0M37 IBD1M37 IBD2M37 LDL1 LDL2; DEFINITION IBD0M37 IBD1M37 IBD2M37; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY37 Note: Opening #include file 1 specify37 SPECIFY K IBD0M37 IBD1M37 IBD2M37 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M37 IBD1M37 IBD0M37 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.218 0.513 0.269 3.558 3.632 Variance 0.120 0.136 0.127 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.985 0.974 0.988 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.330 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.248 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.666 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.444 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.323 0.000 0.434 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.330 0.000 0.444 0.248 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.022 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.575 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.498 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.330 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.248 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.666 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.444 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.323 0.000 0.434 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.330 0.000 0.444 0.248 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.022 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.575 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.498 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.330 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.248 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.184 2 0.646 3 0.170 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.666 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.493 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.444 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.323 0.000 0.434 0.243 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.330 0.000 0.444 0.248 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.022 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.575 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.498 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1096.728 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.52 Execution 0: 0: 0:-1.08 TOTAL 0: 0: 0: 1.44 Total number of warnings issued: 32 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M37 IBD1M37 IBD0M37 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.218 0.513 0.269 3.558 3.632 Variance 0.120 0.136 0.127 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.985 0.974 0.988 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.184 2 0.646 3 0.170 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.493 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1096.728 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 3.110 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.078 Akaike's Information Criterion > 1.110 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.47 TOTAL 0: 0: 0: 1.47 Total number of warnings issued: 32 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF38 Note: Opening #include file 1 seldef38 SELECT IBD0M38 IBD1M38 IBD2M38 LDL1 LDL2; DEFINITION IBD0M38 IBD1M38 IBD2M38; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY38 Note: Opening #include file 1 specify38 SPECIFY K IBD0M38 IBD1M38 IBD2M38 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M38 IBD1M38 IBD0M38 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.216 0.524 0.260 3.558 3.632 Variance 0.107 0.117 0.113 1.012 1.164 Minimum 0.000 0.014 0.000 0.000 0.000 Maximum 0.980 0.968 0.986 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.364 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.641 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.411 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.356 0.000 0.402 0.242 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.364 0.000 0.411 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.023 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.604 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.497 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.364 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.641 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.411 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.356 0.000 0.402 0.242 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.364 0.000 0.411 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.023 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.604 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.497 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.364 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.112 2 0.554 3 0.334 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.641 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.611 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.411 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.356 0.000 0.402 0.242 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.364 0.000 0.411 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.023 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.604 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.497 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1097.377 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 3.44 Execution 0: 0: 0:-1.14 TOTAL 0: 0: 0: 2.30 Total number of warnings issued: 32 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M38 IBD1M38 IBD0M38 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.216 0.524 0.260 3.558 3.632 Variance 0.107 0.117 0.113 1.012 1.164 Minimum 0.000 0.014 0.000 0.000 0.000 Maximum 0.980 0.968 0.986 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.112 2 0.554 3 0.334 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.611 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1097.377 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 2.461 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.117 Akaike's Information Criterion > 0.461 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.94 TOTAL 0: 0: 0: 1.94 Total number of warnings issued: 32 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF39 Note: Opening #include file 1 seldef39 SELECT IBD0M39 IBD1M39 IBD2M39 LDL1 LDL2; DEFINITION IBD0M39 IBD1M39 IBD2M39; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY39 Note: Opening #include file 1 specify39 SPECIFY K IBD0M39 IBD1M39 IBD2M39 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M39 IBD1M39 IBD0M39 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.215 0.534 0.251 3.558 3.632 Variance 0.107 0.116 0.107 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.982 0.974 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.423 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.596 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.355 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.413 0.000 0.346 0.241 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.423 0.000 0.355 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.025 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.651 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.497 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.423 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.596 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.355 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.413 0.000 0.346 0.241 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.423 0.000 0.355 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.025 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.651 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.497 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.423 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.247 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.059 2 0.423 3 0.518 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.596 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.635 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.730 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.355 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.413 0.000 0.346 0.241 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.423 0.000 0.355 0.247 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.025 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.651 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.497 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.065 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.31 Execution 0: 0: 0: 0.41 TOTAL 0: 0: 0: 2.72 Total number of warnings issued: 32 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M39 IBD1M39 IBD0M39 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.215 0.534 0.251 3.558 3.632 Variance 0.107 0.116 0.107 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.982 0.974 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.059 2 0.423 3 0.518 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.730 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.065 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.773 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.183 Akaike's Information Criterion > -0.227 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.54 TOTAL 0: 0: 0: 1.54 Total number of warnings issued: 32 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF40 Note: Opening #include file 1 seldef40 SELECT IBD0M40 IBD1M40 IBD2M40 LDL1 LDL2; DEFINITION IBD0M40 IBD1M40 IBD2M40; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY40 Note: Opening #include file 1 specify40 SPECIFY K IBD0M40 IBD1M40 IBD2M40 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M40 IBD1M40 IBD0M40 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.214 0.542 0.244 3.558 3.632 Variance 0.121 0.133 0.108 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.990 0.995 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.499 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.530 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.281 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.486 0.000 0.274 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.499 0.000 0.281 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.706 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.499 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.530 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.281 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.486 0.000 0.274 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.499 0.000 0.281 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.706 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.499 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.024 2 0.251 3 0.724 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.530 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.850 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.281 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.486 0.000 0.274 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.499 0.000 0.281 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.706 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.697 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.71 Execution 0: 0: 0: 1.60 TOTAL 0: 0: 0: 3.31 Total number of warnings issued: 32 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M40 IBD1M40 IBD0M40 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.214 0.542 0.244 3.558 3.632 Variance 0.121 0.133 0.108 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.990 0.995 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.024 2 0.251 3 0.724 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.850 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.697 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.141 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.285 Akaike's Information Criterion > -0.859 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.54 TOTAL 0: 0: 0: 1.54 Total number of warnings issued: 32 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF41 Note: Opening #include file 1 seldef41 SELECT IBD0M41 IBD1M41 IBD2M41 LDL1 LDL2; DEFINITION IBD0M41 IBD1M41 IBD2M41; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY41 Note: Opening #include file 1 specify41 SPECIFY K IBD0M41 IBD1M41 IBD2M41 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M41 IBD1M41 IBD0M41 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.218 0.537 0.245 3.558 3.632 Variance 0.110 0.112 0.098 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.975 0.969 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.493 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.537 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.288 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.480 0.000 0.281 0.239 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.493 0.000 0.288 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.027 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.702 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.493 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.537 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.288 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.480 0.000 0.281 0.239 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.493 0.000 0.288 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.027 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.702 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.493 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.016 2 0.205 3 0.779 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.537 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.881 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.288 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.480 0.000 0.281 0.239 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.493 0.000 0.288 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.027 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.702 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.746 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.94 Execution 0: 0: 0: 0.28 TOTAL 0: 0: 0: 3.22 Total number of warnings issued: 34 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M41 IBD1M41 IBD0M41 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.218 0.537 0.245 3.558 3.632 Variance 0.110 0.112 0.098 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.975 0.969 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.016 2 0.205 3 0.779 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.881 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.746 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.092 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.296 Akaike's Information Criterion > -0.908 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.87 TOTAL 0: 0: 0: 1.87 Total number of warnings issued: 34 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF42 Note: Opening #include file 1 seldef42 SELECT IBD0M42 IBD1M42 IBD2M42 LDL1 LDL2; DEFINITION IBD0M42 IBD1M42 IBD2M42; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY42 Note: Opening #include file 1 specify42 SPECIFY K IBD0M42 IBD1M42 IBD2M42 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M42 IBD1M42 IBD0M42 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.221 0.532 0.247 3.558 3.632 Variance 0.101 0.096 0.092 1.012 1.164 Minimum 0.000 0.017 0.000 0.000 0.000 Maximum 0.963 0.950 0.983 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.484 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.004 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.543 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.295 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.471 0.004 0.287 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.484 0.004 0.295 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.028 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.696 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.064 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.484 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.004 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.543 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.295 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.471 0.004 0.287 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.484 0.004 0.295 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.028 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.696 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.064 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.484 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.004 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.011 2 0.173 3 0.815 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.543 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.902 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.295 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.471 0.004 0.287 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.484 0.004 0.295 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.028 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.696 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.064 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.762 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.31 Execution 0: 0: 0: 0.28 TOTAL 0: 0: 0: 2.59 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M42 IBD1M42 IBD0M42 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.221 0.532 0.247 3.558 3.632 Variance 0.101 0.096 0.092 1.012 1.164 Minimum 0.000 0.017 0.000 0.000 0.000 Maximum 0.963 0.950 0.983 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.011 2 0.173 3 0.815 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.902 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.762 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.076 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.300 Akaike's Information Criterion > -0.924 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.25 TOTAL 0: 0: 0: 1.25 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF43 Note: Opening #include file 1 seldef43 SELECT IBD0M43 IBD1M43 IBD2M43 LDL1 LDL2; DEFINITION IBD0M43 IBD1M43 IBD2M43; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY43 Note: Opening #include file 1 specify43 SPECIFY K IBD0M43 IBD1M43 IBD2M43 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M43 IBD1M43 IBD0M43 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.224 0.529 0.247 3.558 3.632 Variance 0.100 0.092 0.089 1.012 1.164 Minimum 0.000 0.017 0.000 0.000 0.000 Maximum 0.959 0.949 0.983 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.483 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.015 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.536 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.287 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.469 0.015 0.278 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.483 0.015 0.287 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.030 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.695 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.123 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.483 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.015 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.536 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.287 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.469 0.015 0.278 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.483 0.015 0.287 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.030 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.695 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.123 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.483 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.015 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.006 2 0.136 3 0.858 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.536 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.633 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.926 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.287 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.469 0.015 0.278 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.483 0.015 0.287 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.030 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.695 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.123 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.816 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.18 Execution 0: 0: 0: 0.87 TOTAL 0: 0: 0: 3.05 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M43 IBD1M43 IBD0M43 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.224 0.529 0.247 3.558 3.632 Variance 0.100 0.092 0.089 1.012 1.164 Minimum 0.000 0.017 0.000 0.000 0.000 Maximum 0.959 0.949 0.983 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.006 2 0.136 3 0.858 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.926 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.816 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.022 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.312 Akaike's Information Criterion > -0.978 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.02 TOTAL 0: 0: 0: 1.02 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF44 Note: Opening #include file 1 seldef44 SELECT IBD0M44 IBD1M44 IBD2M44 LDL1 LDL2; DEFINITION IBD0M44 IBD1M44 IBD2M44; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY44 Note: Opening #include file 1 specify44 SPECIFY K IBD0M44 IBD1M44 IBD2M44 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M44 IBD1M44 IBD0M44 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.226 0.527 0.247 3.558 3.632 Variance 0.105 0.098 0.092 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.965 0.964 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.493 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.025 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.518 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.268 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.477 0.025 0.260 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.493 0.025 0.268 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.702 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.160 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.493 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.025 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.518 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.268 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.477 0.025 0.260 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.493 0.025 0.268 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.702 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.160 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.493 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.025 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.003 2 0.090 3 0.907 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.518 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.952 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.268 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.477 0.025 0.260 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.493 0.025 0.268 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.702 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.160 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.899 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.80 Execution 0: 0: 0:-0.04 TOTAL 0: 0: 0: 2.76 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M44 IBD1M44 IBD0M44 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.226 0.527 0.247 3.558 3.632 Variance 0.105 0.098 0.092 1.012 1.164 Minimum 0.000 0.011 0.000 0.000 0.000 Maximum 0.965 0.964 0.989 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.003 2 0.090 3 0.907 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.952 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.899 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.939 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.333 Akaike's Information Criterion > -1.061 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.82 TOTAL 0: 0: 0: 1.82 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF45 Note: Opening #include file 1 seldef45 SELECT IBD0M45 IBD1M45 IBD2M45 LDL1 LDL2; DEFINITION IBD0M45 IBD1M45 IBD2M45; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY45 Note: Opening #include file 1 specify45 SPECIFY K IBD0M45 IBD1M45 IBD2M45 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M45 IBD1M45 IBD0M45 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.226 0.527 0.246 3.558 3.632 Variance 0.115 0.110 0.096 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.973 0.992 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.508 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.033 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.496 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.246 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.492 0.032 0.238 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.508 0.033 0.246 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.713 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.182 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.508 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.033 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.496 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.246 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.492 0.032 0.238 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.508 0.033 0.246 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.713 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.182 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.508 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.033 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.042 3 0.957 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.496 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.632 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.978 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.246 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.492 0.032 0.238 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.508 0.033 0.246 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.713 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.182 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.998 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.47 Execution 0: 0: 0:-0.01 TOTAL 0: 0: 0: 2.46 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M45 IBD1M45 IBD0M45 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.226 0.527 0.246 3.558 3.632 Variance 0.115 0.110 0.096 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.973 0.992 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.042 3 0.957 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.978 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.998 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.840 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.359 Akaike's Information Criterion > -1.160 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.10 TOTAL 0: 0: 0: 1.10 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF46 Note: Opening #include file 1 seldef46 SELECT IBD0M46 IBD1M46 IBD2M46 LDL1 LDL2; DEFINITION IBD0M46 IBD1M46 IBD2M46; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY46 Note: Opening #include file 1 specify46 SPECIFY K IBD0M46 IBD1M46 IBD2M46 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M46 IBD1M46 IBD0M46 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.231 0.527 0.242 3.558 3.632 Variance 0.103 0.087 0.080 1.012 1.164 Minimum 0.000 0.017 0.001 0.000 0.000 Maximum 0.957 0.958 0.983 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.512 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.030 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.496 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.246 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.495 0.029 0.238 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.512 0.030 0.246 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.715 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.172 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.512 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.030 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.496 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.246 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.495 0.029 0.238 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.512 0.030 0.246 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.715 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.172 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.512 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.030 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.054 3 0.945 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.496 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.972 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.246 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.495 0.029 0.238 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.512 0.030 0.246 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.715 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.172 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.095 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.99 Execution 0: 0: 0: 0.40 TOTAL 0: 0: 0: 2.39 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M46 IBD1M46 IBD0M46 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.231 0.527 0.242 3.558 3.632 Variance 0.103 0.087 0.080 1.012 1.164 Minimum 0.000 0.017 0.001 0.000 0.000 Maximum 0.957 0.958 0.983 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.054 3 0.945 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.972 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.095 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.743 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.389 Akaike's Information Criterion > -1.257 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.18 TOTAL 0: 0: 0: 1.18 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF47 Note: Opening #include file 1 seldef47 SELECT IBD0M47 IBD1M47 IBD2M47 LDL1 LDL2; DEFINITION IBD0M47 IBD1M47 IBD2M47; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY47 Note: Opening #include file 1 specify47 SPECIFY K IBD0M47 IBD1M47 IBD2M47 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M47 IBD1M47 IBD0M47 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.235 0.527 0.238 3.558 3.632 Variance 0.099 0.076 0.072 1.012 1.164 Minimum 0.000 0.026 0.001 0.000 0.000 Maximum 0.947 0.935 0.974 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.531 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.026 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.480 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.230 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.514 0.025 0.223 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.531 0.026 0.230 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.729 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.161 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.531 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.026 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.480 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.230 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.514 0.025 0.223 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.531 0.026 0.230 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.729 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.161 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.531 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.026 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.060 3 0.939 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.480 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.631 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.969 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.230 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.514 0.025 0.223 0.237 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.531 0.026 0.230 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.033 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.729 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.161 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.232 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 3.10 Execution 0: 0: 0:-1.24 TOTAL 0: 0: 0: 1.86 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M47 IBD1M47 IBD0M47 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.235 0.527 0.238 3.558 3.632 Variance 0.099 0.076 0.072 1.012 1.164 Minimum 0.000 0.026 0.001 0.000 0.000 Maximum 0.947 0.935 0.974 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.060 3 0.939 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.969 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.232 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.606 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.436 Akaike's Information Criterion > -1.394 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.65 TOTAL 0: 0: 0: 0.65 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF48 Note: Opening #include file 1 seldef48 SELECT IBD0M48 IBD1M48 IBD2M48 LDL1 LDL2; DEFINITION IBD0M48 IBD1M48 IBD2M48; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY48 Note: Opening #include file 1 specify48 SPECIFY K IBD0M48 IBD1M48 IBD2M48 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M48 IBD1M48 IBD0M48 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.240 0.526 0.234 3.558 3.632 Variance 0.101 0.076 0.070 1.012 1.164 Minimum 0.000 0.029 0.001 0.000 0.000 Maximum 0.944 0.926 0.970 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.565 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.022 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.447 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.630 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.199 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.548 0.021 0.193 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.565 0.022 0.199 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.752 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.149 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.565 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.022 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.447 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.630 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.199 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.548 0.021 0.193 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.565 0.022 0.199 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.752 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.149 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.565 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.022 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.060 3 0.939 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.447 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.630 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.969 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.199 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.548 0.021 0.193 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.565 0.022 0.199 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.752 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.149 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.390 Degrees of freedom >>>>>>>>>>>>>>>> 413 !@machine; OPTIONS 3 0 0 0 ; GLOBAL_OPTIONS 80 3 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 0 0.000000000000000E+00 0 0 1.05000000E-08 1000 0.899999976 3.25999991E-12 1.00000002E+20 4.37000010E-15 0 0 0 0 0 0 0 -1 -1.000000000000000 "" ; This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.64 Execution 0: 0: 0:-0.75 TOTAL 0: 0: 0: 1.89 Total number of warnings issued: 36 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M48 IBD1M48 IBD0M48 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.240 0.526 0.234 3.558 3.632 Variance 0.101 0.076 0.070 1.012 1.164 Minimum 0.000 0.029 0.001 0.000 0.000 Maximum 0.944 0.926 0.970 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.060 3 0.939 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.969 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.390 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.448 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.503 Akaike's Information Criterion > -1.552 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.43 TOTAL 0: 0: 0: 1.43 Total number of warnings issued: 36 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF49 Note: Opening #include file 1 seldef49 SELECT IBD0M49 IBD1M49 IBD2M49 LDL1 LDL2; DEFINITION IBD0M49 IBD1M49 IBD2M49; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY49 Note: Opening #include file 1 specify49 SPECIFY K IBD0M49 IBD1M49 IBD2M49 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M49 IBD1M49 IBD0M49 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.245 0.525 0.231 3.558 3.632 Variance 0.111 0.086 0.073 1.012 1.164 Minimum 0.000 0.026 0.001 0.000 0.000 Maximum 0.945 0.933 0.974 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.609 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.019 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.398 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.630 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.159 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.590 0.019 0.154 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.609 0.019 0.159 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.780 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.139 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.609 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.019 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.398 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.630 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.159 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.590 0.019 0.154 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.609 0.019 0.159 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.780 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.139 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.609 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.019 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.055 3 0.944 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.398 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.630 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.972 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.159 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.590 0.019 0.154 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.609 0.019 0.159 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.780 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.139 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.542 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 4.09 Execution 0: 0: 0:-1.33 TOTAL 0: 0: 0: 2.76 Total number of warnings issued: 38 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M49 IBD1M49 IBD0M49 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.245 0.525 0.231 3.558 3.632 Variance 0.111 0.086 0.073 1.012 1.164 Minimum 0.000 0.026 0.001 0.000 0.000 Maximum 0.945 0.933 0.974 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.055 3 0.944 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.972 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.542 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.296 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.586 Akaike's Information Criterion > -1.704 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.98 TOTAL 0: 0: 0: 0.98 Total number of warnings issued: 38 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF50 Note: Opening #include file 1 seldef50 SELECT IBD0M40 IBD1M40 IBD2M40 LDL1 LDL2; DEFINITION IBD0M40 IBD1M40 IBD2M40; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Global variable previously defined. Updating IBD0M40 Note: Global variable previously defined. Updating IBD1M40 Note: Global variable previously defined. Updating IBD2M40 Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY50 Note: Opening #include file 1 specify50 SPECIFY K IBD0M40 IBD1M40 IBD2M40 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M40 IBD1M40 IBD0M40 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.214 0.542 0.244 3.558 3.632 Variance 0.121 0.133 0.108 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.990 0.995 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.499 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.530 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.281 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.486 0.000 0.274 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.499 0.000 0.281 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.706 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.499 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.530 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.281 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.486 0.000 0.274 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.499 0.000 0.281 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.706 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.499 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.000 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.246 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.024 2 0.251 3 0.724 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.530 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.634 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.850 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.281 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.486 0.000 0.274 0.240 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.499 0.000 0.281 0.246 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.026 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.706 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.496 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1098.697 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.67 Execution 0: 0: 0: 0.77 TOTAL 0: 0: 0: 2.44 Total number of warnings issued: 38 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M40 IBD1M40 IBD0M40 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.214 0.542 0.244 3.558 3.632 Variance 0.121 0.133 0.108 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.990 0.995 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.024 2 0.251 3 0.724 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.850 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1098.697 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 1.141 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.285 Akaike's Information Criterion > -0.859 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.17 TOTAL 0: 0: 0: 1.17 Total number of warnings issued: 38 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF51 Note: Opening #include file 1 seldef51 SELECT IBD0M51 IBD1M51 IBD2M51 LDL1 LDL2; DEFINITION IBD0M51 IBD1M51 IBD2M51; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY51 Note: Opening #include file 1 specify51 SPECIFY K IBD0M51 IBD1M51 IBD2M51 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M51 IBD1M51 IBD0M51 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.256 0.520 0.224 3.558 3.632 Variance 0.157 0.144 0.097 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.974 0.986 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.694 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.016 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.276 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.076 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.672 0.016 0.074 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.694 0.016 0.076 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.833 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.128 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.694 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.016 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.276 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.076 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.672 0.016 0.074 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.694 0.016 0.076 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.833 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.128 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.694 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.016 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.000 2 0.026 3 0.974 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.276 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.987 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.076 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.672 0.016 0.074 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.694 0.016 0.076 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.833 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.128 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.750 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.22 Execution 0: 0: 0: 1.73 TOTAL 0: 0: 0: 3.95 Total number of warnings issued: 40 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M51 IBD1M51 IBD0M51 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.256 0.520 0.224 3.558 3.632 Variance 0.157 0.144 0.097 1.012 1.164 Minimum 0.000 0.002 0.000 0.000 0.000 Maximum 0.974 0.986 0.998 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.000 2 0.026 3 0.974 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.987 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.750 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.088 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.767 Akaike's Information Criterion > -1.912 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.71 TOTAL 0: 0: 0: 1.71 Total number of warnings issued: 40 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF52 Note: Opening #include file 1 seldef52 SELECT IBD0M52 IBD1M52 IBD2M52 LDL1 LDL2; DEFINITION IBD0M52 IBD1M52 IBD2M52; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY52 Note: Opening #include file 1 specify52 SPECIFY K IBD0M52 IBD1M52 IBD2M52 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M52 IBD1M52 IBD0M52 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.517 0.224 3.558 3.632 Variance 0.140 0.119 0.085 1.012 1.164 Minimum 0.001 0.047 0.001 0.000 0.000 Maximum 0.931 0.942 0.953 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.701 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.263 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.069 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.679 0.016 0.067 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.701 0.017 0.069 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.837 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.701 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.263 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.069 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.679 0.016 0.067 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.701 0.017 0.069 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.837 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.701 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.071 3 0.928 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.263 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.963 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.069 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.679 0.016 0.067 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.701 0.017 0.069 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.837 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.771 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 4.72 Execution 0: 0: 0:-1.34 TOTAL 0: 0: 0: 3.38 Total number of warnings issued: 40 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M52 IBD1M52 IBD0M52 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.517 0.224 3.558 3.632 Variance 0.140 0.119 0.085 1.012 1.164 Minimum 0.001 0.047 0.001 0.000 0.000 Maximum 0.931 0.942 0.953 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.001 2 0.071 3 0.928 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.963 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.771 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.067 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.796 Akaike's Information Criterion > -1.933 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.72 TOTAL 0: 0: 0: 1.72 Total number of warnings issued: 40 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF53 Note: Opening #include file 1 seldef53 SELECT IBD0M53 IBD1M53 IBD2M53 LDL1 LDL2; DEFINITION IBD0M53 IBD1M53 IBD2M53; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY53 Note: Opening #include file 1 specify53 SPECIFY K IBD0M53 IBD1M53 IBD2M53 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M53 IBD1M53 IBD0M53 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.515 0.227 3.558 3.632 Variance 0.114 0.087 0.071 1.012 1.164 Minimum 0.004 0.114 0.005 0.000 0.000 Maximum 0.863 0.876 0.883 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.695 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.274 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.075 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.674 0.016 0.073 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.695 0.017 0.075 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.834 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.695 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.274 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.075 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.674 0.016 0.073 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.695 0.017 0.075 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.834 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.695 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.005 2 0.134 3 0.861 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.274 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.928 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.075 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.674 0.016 0.073 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.695 0.017 0.075 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.834 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.771 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 4.93 Execution 0: 0: 0:-1.39 TOTAL 0: 0: 0: 3.54 Total number of warnings issued: 40 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M53 IBD1M53 IBD0M53 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.515 0.227 3.558 3.632 Variance 0.114 0.087 0.071 1.012 1.164 Minimum 0.004 0.114 0.005 0.000 0.000 Maximum 0.863 0.876 0.883 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.005 2 0.134 3 0.861 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.928 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.771 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.067 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.796 Akaike's Information Criterion > -1.933 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.80 TOTAL 0: 0: 0: 1.80 Total number of warnings issued: 40 ______________________________________________________________________________ The following MX script lines were read for group 1 #DEFINE NVAR 1 Note: Global variable previously defined. Updated: NVAR #DEFINE NSIB 2 !NUMBER OF SIBLINGS Note: Global variable previously defined. Updated: NSIB #NGROUPS 3 Note: #NGroup set number of groups to 3 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER L FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS U UNIT 1 NSIB H FULL 1 1 END MATRICES; MATRIX H .5 BEGIN ALGEBRA; A= X*X'; !ADDITIVE GENETIC VARIANCE C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= A+C+Q+E; !TOTAL VARIANCE T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 C^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 C^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: MZ TWINS #INCLUDE LIPIDMZ.DAT Note: Opening #include file 1 lipidmz.dat DATA NINPUTVARS=14 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDMZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 92 records with data that contained a total of 1288 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1 NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2 Note: Closing #include file 1 SELECT LDL1 LDL2; BEGIN MATRICES = GROUP 1; NOTE: Selection yields 92 data vectors for analysis NOTE: Vectors contain a total of 184 observations MEANS U@M; COVARIANCE A+C+Q+E | A+C+Q _ A+C+Q | A+C+Q+E; END The following MX script lines were read for group 3 G3: DIZYGOTIC TWINS #INCLUDE LIPIDDZ.DAT Note: Opening #include file 1 lipiddz.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21286 observations MISSING=-1.00 NOTE: Missing value *string* set to '-1.00' LABELS FAM ZYG1_5 NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1 NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2 PIHAT65 PI65CAT IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 #INCLUDE SELDEF54 Note: Opening #include file 1 seldef54 SELECT IBD0M54 IBD1M54 IBD2M54 LDL1 LDL2; DEFINITION IBD0M54 IBD1M54 IBD2M54; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 585 observations Note: Closing #include file 1 BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 234 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT END MATRICES; #INCLUDE SPECIFY54 Note: Opening #include file 1 specify54 SPECIFY K IBD0M54 IBD1M54 IBD2M54 Note: Closing #include file 1 MATRIX J 0. 0.5 1.0 BEGIN ALGEBRA; P= J*K; !ESTIMATE OF PIHAT END ALGEBRA; MEANS U@M; COVARIANCE A+C+Q+E | H@A+C+P@Q _ H@A+C+P@Q | A+C+Q+E; START 1 ALL START 2.8 M 1 1 1 OPTION NDECIMALS=3 OPTION MULTIPLE ISSAT END Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M54 IBD1M54 IBD0M54 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.514 0.228 3.558 3.632 Variance 0.103 0.074 0.064 1.012 1.164 Minimum 0.006 0.144 0.008 0.000 0.000 Maximum 0.832 0.848 0.850 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 5 *** WARNING! *** I am not sure I have found a solution that satisfies Kuhn-Tucker conditions for a minimum. NAG's IFAIL parameter is 1 We probably have a minimum here, but you might consider trying different starting values. You can randomize these with TH=n on the OU line, where n is the number of times you wish to do this. I STRONGLY recommend BOundaries to be set if you use TH MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.692 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.279 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.078 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.671 0.016 0.075 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.692 0.017 0.078 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.832 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.692 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.279 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.078 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.671 0.016 0.075 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.692 0.017 0.078 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.832 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.692 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.017 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.008 2 0.162 3 0.830 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.279 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.911 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.078 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.671 0.016 0.075 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.692 0.017 0.078 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.032 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.832 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.129 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.771 Degrees of freedom >>>>>>>>>>>>>>>> 413 This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 4.73 Execution 0: 0: 0:-1.15 TOTAL 0: 0: 0: 3.58 Total number of warnings issued: 42 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 2 LDL1 LDL2 Code 1.000 2.000 Number 92.000 92.000 Mean 3.648 3.719 Variance 1.100 0.749 Minimum 0.000 1.730 Maximum 5.980 5.960 Summary of VL file data for group 3 IBD2M54 IBD1M54 IBD0M54 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 117.000 117.000 Mean 0.259 0.514 0.228 3.558 3.632 Variance 0.103 0.074 0.064 1.012 1.164 Minimum 0.006 0.144 0.008 0.000 0.000 Maximum 0.832 0.848 0.850 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX C This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX M This is a FULL matrix of order 1 by 1 1 1 5 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 3 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 2 G2: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 GROUP NUMBER: 3 G3: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.769 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.018 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.245 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.008 2 0.162 3 0.830 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 3.629 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.911 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 C^2 Q^2 E^2 STANDEST 0.745 0.017 0.000 0.238 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|C|Q|E] A^2 C^2 Q^2 E^2 UNSTANDEST 0.769 0.018 0.000 0.245 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+C+Q+E] 1 1 1.031 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.877 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.133 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.495 Your model has 4 estimated parameters and 418 Observed statistics -2 times log-likelihood of data >>> 1099.838 Degrees of freedom >>>>>>>>>>>>>>>> 414 Saturated model fit* >>>>>>>>>>> 1099.771 Saturated model df* >>>>>>>>>>> 413 Difference Chi-squared >>>>>>>> 0.067 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.796 Akaike's Information Criterion > -1.933 * Saturated model statistic computed earlier in this job This problem used 1.6% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 1.82 TOTAL 0: 0: 0: 1.82 Total number of warnings issued: 42 ______________________________________________________________________________ Note: repeat section completed