** Mx startup successful ** **MX-PC 1.54** Job started on 03/04/03 at 17:59:22 !QTL analysis via Mixture Distribution method !Using marker1 !Using DZ twins only !Analysis of LDL !Dutch Adults The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NSIB 2 !NUMBER OF SIBLINGS #NGROUPS 2 Note: #NGroup set number of groups to 2 G1: PARAMETER ESTIMATES CALCULATION BEGIN MATRICES; X LOWER NVAR NVAR FREE !FAMILIAL BACKGROUND Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL 1 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS H FULL 1 1 END MATRICES; SPECIFY M 10 10 MATRIX H .5 BEGIN ALGEBRA; F= X*X'; !FAMILIAL VARIANCE E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; !VARIANCE DUE TO QTL V= F+Q+E; !TOTAL VARIANCE T= F|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 END The following MX script lines were read for group 2 G2: DIZYGOTIC TWINS #INCLUDE LIPIDDZMIX.DAT Note: Opening #include file 1 lipiddzmix.dat DATA NINPUTVARS=182 NOBSERVATIONS=0 NMODEL=3 RECTANGULAR FILE=LIPIDDZ.REC Rectangular continuous data read initiated NOTE: Rectangular file contained 117 records with data that contained a total of 21292 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 SELECT IBD0M1 IBD1M1 IBD2M1 LDL1 LDL2; DEFINITION IBD0M1 IBD1M1 IBD2M1; NOTE: Selection yields 117 data vectors for analysis NOTE: Vectors contain a total of 583 observations BEGIN MATRICES = GROUP 1; NOTE: Definition yields 117 data vectors for analysis NOTE: Vectors contain a total of 232 observations K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) U UNIT 3 2 END MATRICES; SPECIFY K IBD0M1 IBD1M1 IBD2M1 MEANS U@M; COVARIANCE F+Q+E | F _ F | F+Q+E _ ! IBD 0 COVARIANCE MATRIX F+Q+E | F+ H@Q_ F+H@Q | F+Q+E _ ! IBD 1 COVARIANCE MATRIX F+Q+E | F+Q _ F+Q | F+Q+E; ! IBD 2 COVARIANCE MATRIX WEIGHTS K; ! IBD PROBABILITIES 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 IBD2M1 IBD1M1 IBD0M1 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 116.000 116.000 Mean 0.259 0.501 0.240 3.588 3.663 Variance 0.047 0.020 0.032 0.911 1.059 Minimum 0.027 0.275 0.035 0.580 0.600 Maximum 0.659 0.722 0.697 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It 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 3 MATRIX M This is a FULL matrix of order 1 by 1 1 1 10 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 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 3 MATRIX M This is a FULL matrix of order 1 by 1 1 1 10 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX U This is a UNIT matrix of order 3 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.542 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.443 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 3.626 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 3 [=T@V~] F^2 Q^2 E^2 STANDEST 0.450 0.000 0.550 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 0.443 0.000 0.542 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 0.985 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.666 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.736 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.542 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.443 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 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 3.626 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 3 [=T@V~] F^2 Q^2 E^2 STANDEST 0.450 0.000 0.550 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 0.443 0.000 0.542 MATRIX U This is a UNIT matrix of order 3 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 0.985 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.666 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.736 Your model has 4 estimated parameters and 232 Observed statistics -2 times log-likelihood of data >>> 628.870 Degrees of freedom >>>>>>>>>>>>>>>> 228 Model number: 1 Model number: 2 Model number: 3 This problem used 0.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.44 Execution 0: 0: 0:-0.69 TOTAL 0: 0: 0: 0.75 Total number of warnings issued: 0 ______________________________________________________________________________ ! Test significance of QTL effect Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 END Summary of VL file data for group 2 IBD2M1 IBD1M1 IBD0M1 LDL1 LDL2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 117.000 117.000 117.000 116.000 116.000 Mean 0.259 0.501 0.240 3.588 3.663 Variance 0.047 0.020 0.032 0.911 1.059 Minimum 0.027 0.275 0.035 0.580 0.600 Maximum 0.659 0.722 0.697 5.650 6.390 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Parameter Estimates MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It 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 10 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 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 10 MATRIX Q This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX S This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX U This is a UNIT matrix of order 3 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 3 MX PARAMETER ESTIMATES GROUP NUMBER: 1 G1: Parameter Estimates MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.542 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.443 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 3.626 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 3 [=T@V~] F^2 Q^2 E^2 STANDEST 0.450 0.000 0.550 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 0.443 0.000 0.542 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 0.985 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.666 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.736 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.542 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.443 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 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 3.626 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 3 [=T@V~] F^2 Q^2 E^2 STANDEST 0.450 0.000 0.550 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 0.443 0.000 0.542 MATRIX U This is a UNIT matrix of order 3 by 2 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 0.985 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.666 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.736 Your model has 3 estimated parameters and 232 Observed statistics -2 times log-likelihood of data >>> 628.870 Degrees of freedom >>>>>>>>>>>>>>>> 229 Saturated model fit* >>>>>>>>>>> 628.870 Saturated model df* >>>>>>>>>>> 228 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 Model number: 1 Model number: 2 Model number: 3 This problem used 0.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.08 TOTAL 0: 0: 0: 0.08 Total number of warnings issued: 0 ______________________________________________________________________________