** Mx startup successful ** **MX-PC 1.52** Job started on 03/08/02 at 14:31:09 !David Evans & Nick Martin platelet data ! QTL linkage study of platelet count at age 14, marker 6 !Using MZ and DZ twins The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NSIB 2 ! NUMBER OF SIBLINGS G1: MONOZYGOTIC TWINS DATA NGROUPS=2 NINPUT=9 RECTANGULAR FILE = Y14MARKER6.DAT Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 4331 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT2 PLT22 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2294 observations SELECT PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 287 data vectors for analysis NOTE: Vectors contain a total of 1146 observations NOTE: Definition yields 145 data vectors for analysis NOTE: Vectors contain a total of 285 observations BEGIN MATRICES X LOWER NVAR NVAR FREE !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR FREE !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT L FULL NVAR 1 FREE !QTL EFFECT M FULL NVAR 1 FREE !MEANS END MATRICES BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_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 2 G2: DIZYGOTIC TWINS DATA NINPUT=9 RECTANGULAR FILE = Y14MARKER6.DAT Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 4331 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT2 PLT22 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2037 observations SELECT PIBD0 PIBD1 PIBD2 PLT2 PLT22 / DEFINITION PIBD0 PIBD1 PIBD2 / NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 1109 observations Note: Global variable previously defined. Updating PIBD0 Note: Global variable previously defined. Updating PIBD1 Note: Global variable previously defined. Updating PIBD2 NOTE: Definition yields 208 data vectors for analysis NOTE: Vectors contain a total of 413 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 !ADDITIVE GENETIC BACKGROUND Y LOWER NVAR NVAR =Y1 !COMMON ENVIRONMENTAL EFFECTS Z LOWER NVAR NVAR =Z1 !UNIQUE ENVIRONMENT L FULL NVAR 1 =L1 !QTL EFFECT M FULL NVAR 1 =M1 !MEANS K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; A = X*X'; !ADDITIVE GENETIC VARIANCE C = Y*Y'; !COMMON ENVIRONMENTAL VARIANCE E = Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE Q = L*L'; !VARIANCE DUE TO QTL P = F*K; !ESTIMATE OF PI HAT V = A + Q + C + E; !TOTAL VARIANCE T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 C^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T A^2 Q^2 D^2 E^2 MEANS M_M ; COVARIANCE A+C+Q+E|H@A+C+P@Q_ H@A+C+P@Q|A+C+Q+E; ST 10 X 1 1 1 !START VALUES ST 10 Y 1 1 1 ST 10 Z 1 1 1 ST 10 L 1 1 1 ST 285 M 1 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT END Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 269.607 271.136 Variance 0.000 0.000 0.000 3559.204 3070.317 Minimum 1.000 0.000 0.000 115.000 122.000 Maximum 1.000 0.000 0.000 436.000 428.000 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 208.000 208.000 208.000 207.000 206.000 Mean 0.259 0.474 0.267 266.725 262.951 Variance 0.138 0.135 0.128 2952.035 3594.202 Minimum 0.000 0.000 0.000 131.000 138.000 Maximum 1.000 1.000 1.000 435.000 478.000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic 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 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 V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: 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 F This is a FULL matrix of order 1 by 3 It 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 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 V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 985.795 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 313.395 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 650.958 MATRIX L This is a FULL matrix of order 1 by 1 1 1 36.702 MATRIX M This is a FULL matrix of order 1 by 1 1 1 267.287 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 1347.049 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.299 0.409 0.095 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 985.795 1347.049 313.395 650.958 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 3297.197 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 31.397 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 17.703 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 25.514 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 985.795 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 313.395 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 650.958 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 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 0.001 2 0.184 3 0.814 MATRIX L This is a FULL matrix of order 1 by 1 1 1 36.702 MATRIX M This is a FULL matrix of order 1 by 1 1 1 267.287 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.906 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 1347.049 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.299 0.409 0.095 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 985.795 1347.049 313.395 650.958 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 3297.197 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 31.397 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 17.703 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 25.514 Vector of OBSERVED means PLT2 PLT22 Mean 266.725 262.951 Vector of EXPECTED means PLT2 PLT22 Mean 267.287 267.287 EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 3297.197 PLT22 2027.358 3297.197 Function value of this group: 4463.947 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 698 Observed statistics -2 times log-likelihood of data >>> 7438.152 Degrees of freedom >>>>>>>>>>>>>>>> 693 This problem used 10.9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 1.26 Execution 0: 0: 0:18.08 TOTAL 0: 0: 0:19.34 Total number of warnings issued: 0 ______________________________________________________________________________ Multiple fit option in effect. The following MX script lines have been read: DROP @.0 4 END Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 145.000 145.000 145.000 145.000 140.000 Mean 1.000 0.000 0.000 269.607 271.136 Variance 0.000 0.000 0.000 3559.204 3070.317 Minimum 1.000 0.000 0.000 115.000 122.000 Maximum 1.000 0.000 0.000 436.000 428.000 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT2 PLT22 Code -3.000 -2.000 -1.000 1.000 2.000 Number 208.000 208.000 208.000 207.000 206.000 Mean 0.259 0.474 0.267 266.725 262.951 Variance 0.138 0.135 0.128 2952.035 3594.202 Minimum 0.000 0.000 0.000 131.000 138.000 Maximum 1.000 1.000 1.000 435.000 478.000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: Monozygotic 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 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 V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: 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 F This is a FULL matrix of order 1 by 3 It 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 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 V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: Monozygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 2374.130 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 275.110 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 650.989 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 1 266.994 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 Q^2 C^2 E^2 STANDEST 0.719 0.000 0.083 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 2374.130 0.000 275.110 650.989 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 3300.229 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 48.725 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 16.586 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 25.514 GROUP NUMBER: 2 G2: Dizygotic twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 2374.130 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 275.110 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 650.989 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 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 0.001 2 0.184 3 0.814 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 1 266.994 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.906 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 Q^2 C^2 E^2 STANDEST 0.719 0.000 0.083 0.197 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 D^2 E^2 UNSTANDEST 2374.130 0.000 275.110 650.989 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 3300.229 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 48.725 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 16.586 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 25.514 Vector of OBSERVED means PLT2 PLT22 Mean 266.725 262.951 Vector of EXPECTED means PLT2 PLT22 Mean 266.994 266.994 EXPECTED COVARIANCE MATRIX PLT2 PLT22 PLT2 3300.229 PLT22 1462.175 3300.229 Function value of this group: 4472.008 Where the fit function is -2 * Log-likelihood of raw data Your model has 4 estimated parameters and 698 Observed statistics -2 times log-likelihood of data >>> 7446.308 Degrees of freedom >>>>>>>>>>>>>>>> 694 Saturated model fit* >>>>>>>>>>> 7438.152 Saturated model df* >>>>>>>>>>> 693 Difference Chi-squared >>>>>>>> 8.156 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.004 Akaike's Information Criterion > 6.156 * Saturated model statistic computed earlier in this job This problem used 10.9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 6.64 TOTAL 0: 0: 0: 6.64 Total number of warnings issued: 0 ______________________________________________________________________________