!Analysis of platelet data !QTL linkage study of platelet count at age 14, marker 6 !Using MZ and DZ twins !QTL analysis via weighted likelihood of three covariance matrices The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NSIB 2 ! NUMBER OF SIBLINGS #repeat 8 Note: beginning of #Repeat section G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER1 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER1 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 observations NOTE: Definition yields 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2559 0.4795 0.2646 2.4774 2.4906 Variance 0.1605 0.1711 0.1434 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 0.9965 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1953 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0183 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -1.3132E-07 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5206 2.5206 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 1.7246E-14 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 7.1777E-01 6.3379E-14 6.7108E-02 2.1512E-01 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 1.9531E-01 1.7246E-14 1.8261E-02 5.8538E-02 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2721 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4419 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1351 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1953 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0183 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2721 0.1159 2 0.1159 0.2721 3 0.2721 0.1159 4 0.1159 0.2721 5 0.2721 0.1159 6 0.1159 0.2721 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -1.3132E-07 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5206 2.5206 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.1159 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1159 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1159 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 1.7246E-14 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 7.1777E-01 6.3379E-14 6.7108E-02 2.1512E-01 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 1.9531E-01 1.7246E-14 1.8261E-02 5.8538E-02 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2721 MATRIX W This is a FULL matrix of order 3 by 1 1 1 3.1600E-04 2 3.7583E-02 3 9.6210E-01 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4419 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1351 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 713.513 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0:12.61 Execution 0: 0: 0:***** TOTAL 0: 0: 0: 2.38 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER2 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER2 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2600 0.4604 0.2796 2.4774 2.4906 Variance 0.1492 0.1313 0.1213 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 0.9929 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1112 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0188 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2892 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5218 2.5218 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0836 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4085 0.3073 0.0691 0.2151 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1112 0.0836 0.0188 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2722 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3335 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1372 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2420 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1112 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0188 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2722 0.0744 2 0.0744 0.2722 3 0.2722 0.1162 4 0.1162 0.2722 5 0.2722 0.1581 6 0.1581 0.2722 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2892 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5218 2.5218 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0744 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1162 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1581 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0836 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4085 0.3073 0.0691 0.2151 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1112 0.0836 0.0188 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2722 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.0019 2 0.1619 3 0.8362 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3335 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1372 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2420 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 711.661 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 1.852 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.174 Akaike's Information Criterion > -0.148 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 6.38 Execution 0: 0: 0:-5.96 TOTAL 0: 0: 0: 0.42 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER3 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER3 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2773 0.4283 0.2944 2.4774 2.4906 Variance 0.1706 0.1657 0.1560 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 1.0000 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1342 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0169 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2493 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5219 2.5219 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0622 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4938 0.2287 0.0622 0.2154 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1342 0.0622 0.0169 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2718 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3663 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1300 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1342 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0169 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2718 0.0840 2 0.0840 0.2718 3 0.2718 0.1151 4 0.1151 0.2718 5 0.2718 0.1462 6 0.1462 0.2718 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2493 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5219 2.5219 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0840 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1151 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1462 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0622 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4938 0.2287 0.0622 0.2154 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1342 0.0622 0.0169 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2718 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.0378 2 0.9622 3 0.0000 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3663 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1300 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 712.150 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 1.363 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.243 Akaike's Information Criterion > -0.637 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.72 Execution 0: 0: 0:-2.31 TOTAL 0: 0: 0: 0.41 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER4 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER4 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2722 0.4620 0.2658 2.4774 2.4906 Variance 0.1732 0.1675 0.1370 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 1.0000 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1092 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0132 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3009 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5227 2.5227 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0905 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4024 0.3335 0.0485 0.2156 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1092 0.0905 0.0132 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2715 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3305 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1147 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1092 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0132 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2715 0.0678 2 0.0678 0.2715 3 0.2715 0.1130 4 0.1130 0.2715 5 0.2715 0.1583 6 0.1583 0.2715 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3009 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5227 2.5227 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0678 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1130 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1583 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0905 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4024 0.3335 0.0485 0.2156 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1092 0.0905 0.0132 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2715 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.0717 2 0.8585 3 0.0698 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3305 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1147 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 710.600 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 2.913 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.088 Akaike's Information Criterion > 0.913 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.65 Execution 0: 0: 0:-2.26 TOTAL 0: 0: 0: 0.39 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER5 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER5 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2675 0.4715 0.2609 2.4774 2.4906 Variance 0.1602 0.1585 0.1345 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 0.9954 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.0758 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0149 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3500 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5244 2.5244 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.1225 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.2789 0.4508 0.0549 0.2154 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.0758 0.1225 0.0149 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2717 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2753 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1221 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.0758 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0149 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2717 0.0528 2 0.0528 0.2717 3 0.2717 0.1140 4 0.1140 0.2717 5 0.2717 0.1753 6 0.1753 0.2717 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3500 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5244 2.5244 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0528 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1140 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1753 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.1225 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.2789 0.4508 0.0549 0.2154 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.0758 0.1225 0.0149 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2717 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.1743 2 0.8257 3 0.0000 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2753 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1221 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 708.680 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 4.833 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.028 Akaike's Information Criterion > 2.833 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.71 Execution 0: 0: 0:-2.24 TOTAL 0: 0: 0: 0.47 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER6 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER6 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2594 0.4887 0.2519 2.4774 2.4906 Variance 0.1403 0.1392 0.1205 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 1.0000 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.0293 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 5.1257E-12 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0586 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4267 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5187 2.5187 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.1821 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 1.0843E-01 6.7462E-01 1.8993E-11 2.1695E-01 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 2.9262E-02 1.8207E-01 5.1257E-12 5.8550E-02 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2699 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1711 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -2.2640E-06 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2420 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.0293 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 5.1257E-12 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0586 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2699 0.0146 2 0.0146 0.2699 3 0.2699 0.1057 4 0.1057 0.2699 5 0.2699 0.1967 6 0.1967 0.2699 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.4267 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5187 2.5187 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0146 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1057 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1967 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.1821 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 1.0843E-01 6.7462E-01 1.8993E-11 2.1695E-01 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 2.9262E-02 1.8207E-01 5.1257E-12 5.8550E-02 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2699 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.2780 2 0.7220 3 0.0000 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1711 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -2.2640E-06 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2420 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 703.595 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 9.918 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.002 Akaike's Information Criterion > 7.918 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.66 Execution 0: 0: 0:-2.14 TOTAL 0: 0: 0: 0.52 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER7 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER7 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2661 0.5088 0.2251 2.4774 2.4906 Variance 0.1431 0.1262 0.0935 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 1.0000 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.0942 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0105 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3286 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5208 2.5208 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.1080 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.3473 0.3983 0.0386 0.2158 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.0942 0.1080 0.0105 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2712 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3069 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1024 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.0942 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0105 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2712 0.0576 2 0.0576 0.2712 3 0.2712 0.1116 4 0.1116 0.2712 5 0.2712 0.1656 6 0.1656 0.2712 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3286 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5208 2.5208 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0576 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1116 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1656 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.1080 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.3473 0.3983 0.0386 0.2158 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.0942 0.1080 0.0105 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2712 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.2558 2 0.7442 3 0.0000 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3069 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1024 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 710.002 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 3.511 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.061 Akaike's Information Criterion > 1.511 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.62 Execution 0: 0: 0:-2.21 TOTAL 0: 0: 0: 0.41 Total number of warnings issued: 0 ______________________________________________________________________________ The following MX script lines were read for group 1 G1: MZ TWINS DATA NGROUPS=2 NINPUT=13 RECTANGULAR FILE=MARKER8 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY < 3 / NOTE: Select if yields 287 data vectors for analysis NOTE: Vectors contain a total of 2962 observations SELECT PLT3 PLT23 / BEGIN MATRICES NOTE: Selection yields 172 data vectors for analysis NOTE: Vectors contain a total of 340 observations X LOWER NVAR NVAR FREE ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR FREE ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR FREE ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 FREE ! QTL PATH COEFFICIENTS M FULL NVAR NSIB 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; !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 C^2 E^2 MEANS M ; COVARIANCE A+C+Q+E|A+C+Q_ A+C+Q|A+C+Q+E ; EQ M 1 1 M 1 2 END GROUP; The following MX script lines were read for group 2 G2: DZ TWINS DATA NINPUT=13 NMODEL=3 RECTANGULAR FILE=MARKER8 Rectangular continuous data read initiated NOTE: Rectangular file contained 519 records with data that contained a total of 5624 observations LABELS FAMID INDID1 INDID2 PIBD0 PIBD1 PIBD2 ZYGOSITY PLT1 PLT2 PLT3 PLT21 PLT22 PLT23 SELECT IF ZYGOSITY > 2 / NOTE: Select if yields 232 data vectors for analysis NOTE: Vectors contain a total of 2662 observations SELECT PIBD0 PIBD1 PIBD2 PLT3 PLT23 / DEFINITION PIBD0 PIBD1 PIBD2 / ! WE DON'T NEED THE GENOTYPES FOR LINKAGE NOTE: Selection yields 232 data vectors for analysis NOTE: Vectors contain a total of 941 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 123 data vectors for analysis NOTE: Vectors contain a total of 245 observations BEGIN MATRICES X LOWER NVAR NVAR =X1 ! ADDITIVE GENETIC PATH COEFFICIENTS Y LOWER NVAR NVAR =Y1 ! COMMON ENVIRONMENTAL PATH COEFFICIENTS Z LOWER NVAR NVAR =Z1 ! SPECIFIC ENVIRONMENTAL PATH COEFFICIENTS L LOWER NVAR 1 =L1 ! QTL PATH COEFFICIENTS W FULL 3 1 ! P(I)'S GO HERE M FULL NVAR NSIB = M1 ! MEANS I UNIT 3 1 ! TO SPREAD MEAN OUT FOR ALL MODELS & SIBS H FULL 1 1 END MATRICES MATRIX H .5 SPECIFY W 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 V = A + Q + C + E ; !VARIANCE N = H@A + C ; !IBD 0 COV O = N + H@Q ; !IBD 1 COV P = N + Q ; !IBD 2 COV T = A | Q | C | E; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES K = V|N_ N|V_ ! IBD 0 MATRIX V|O_ O|V_ ! IBD 1 MATRIX V|P_ P|V ; ! IBD 2 MATRIX 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 C^2 E^2 MEANS M_M_M ; COVARIANCE K ; WEIGHTS W ; ST 0.5 ALL ST 2.8 M 1 1 1 OPTION ISSAT OPTION MULTIPLE OPTION SUB 713.513, 581 EXIT; Summary of VL file data for group 1 PLT3 PLT23 Code 1.0000 2.0000 Number 171.0000 169.0000 Mean 2.5406 2.5685 Variance 0.2723 0.2676 Minimum 1.2400 1.5600 Maximum 4.0500 4.0700 Summary of VL file data for group 2 PIBD2 PIBD1 PIBD0 PLT3 PLT23 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 123.0000 123.0000 123.0000 123.0000 122.0000 Mean 0.2603 0.5299 0.2098 2.4774 2.4906 Variance 0.1286 0.1043 0.0674 0.2315 0.3141 Minimum 0.0000 0.0000 0.0000 1.5200 1.4000 Maximum 1.0000 1.0000 1.0000 4.2100 4.1100 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 G1: 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 L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 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: DZ 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 I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 It has no free parameters specified MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 4 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 5 5 MATRIX N This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX O This is a computed FULL matrix of order 1 by 1 It has no free parameters specified 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 W This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Y This is a LOWER TRIANGULAR matrix 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: MZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1353 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0147 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2516 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5212 2.5212 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0633 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4977 0.2329 0.0541 0.2153 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1353 0.0633 0.0147 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2718 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3678 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1213 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 GROUP NUMBER: 2 G2: DZ twins MATRIX A This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 0.1353 MATRIX C This is a computed FULL matrix of order 1 by 1 [=Y*Y'] 1 1 0.0147 MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 0.0585 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX I This is a UNIT matrix of order 3 by 1 MATRIX K This is a computed FULL matrix of order 6 by 2 [=V|N_N|V_V|O_O|V_V|P_P|V] 1 2 1 0.2718 0.0823 2 0.0823 0.2718 3 0.2718 0.1140 4 0.1140 0.2718 5 0.2718 0.1457 6 0.1457 0.2718 MATRIX L This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.2516 MATRIX M This is a FULL matrix of order 1 by 2 1 2 1 2.5212 2.5212 MATRIX N This is a computed FULL matrix of order 1 by 1 [=H@A+C] 1 1 0.0823 MATRIX O This is a computed FULL matrix of order 1 by 1 [=N+H@Q] 1 1 0.1140 MATRIX P This is a computed FULL matrix of order 1 by 1 [=N+Q] 1 1 0.1457 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0633 MATRIX S This is a computed FULL matrix of order 1 by 4 [=T@V~] A^2 Q^2 C^2 E^2 STANDEST 0.4977 0.2329 0.0541 0.2153 MATRIX T This is a computed FULL matrix of order 1 by 4 [=A|Q|C|E] A^2 Q^2 C^2 E^2 UNSTANDEST 0.1353 0.0633 0.0147 0.0585 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A+Q+C+E] 1 1 0.2718 MATRIX W This is a FULL matrix of order 3 by 1 1 1 0.1955 2 0.8045 3 0.0000 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.3678 MATRIX Y This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.1213 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.2419 *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 5 estimated parameters and 585 Observed statistics -2 times log-likelihood of data >>> 712.589 Degrees of freedom >>>>>>>>>>>>>>>> 580 Submodel fit* >>>>>>>>>>> 713.513 Submodel df* >>>>>>>>>>> 581 Difference Chi-squared >>>>>>>> 0.924 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.336 Akaike's Information Criterion > -1.076 * Submodel statistic supplied by user Model number: 1 Model number: 2 Model number: 3 Model number: 1 Model number: 2 Model number: 3 This problem used 1.4% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.79 Execution 0: 0: 0:-2.38 TOTAL 0: 0: 0: 0.41 Total number of warnings issued: 2 ______________________________________________________________________________ Note: repeat section completed The following MX script lines were read for group 1 END