** Mx startup successful ** **MX-Linux version 1.49** ! The dataset is limited to DZ twin pairs only ! The following MX script lines were read for group 1 #DEFINE NVAR 1 #DEFINE NVARX2 2 #NGROUPS 1 Note: #NGroup set number of groups to 1 SIMULATED DATA, REAL ALLELE EFFECT DATA NINPUT=7 ! 7 INPUT VARIABLES RECTANGULAR FILE=SET1.REC ! READ DATA FROM FILE NOTE: Rectangular file contained 1000 records with data LABELS P1 P2 A1S1 A2S1 A1S2 A2S2 TYPE ! aisj is allele i of sibling j ! type is coded: 1: AAAA 2: AAAa 3: AAaa ! 4: AaAA 5: AaAa 6: Aaaa ! 7: aaAA 8: aaAa 9: aaaa DEFINITION_VARIABLES A1S1 A2S1 A1S2 A2S2 TYPE ; NOTE: Definition yields 1000 data vectors for analysis NOTE: Vectors contain a total of 2000 observations ! only p1 and p2 will be analyzed; other variables define the model BEGIN MATRICES A LOWER NVARX2 NVARX2 FREE ! ADDITIVE GENETIC INFLUENCES , CHOLESKY F FULL 2 1 ! A ALLELE COUNT FOR SIB1 (0,1,2) H FULL 2 1 ! A ALLELE COUNT FOR SIB2 I FULL 1 1 ! TO STORE TYPE J UNIT 1 1 ! 1.0 K FULL 1 1 ! 2.0 U UNIT 1 2 ! UNIT MATRIX B FULL 1 1 ! BETA WEIGHT FOR INDIVIDUAL ALLELE COUNT N FULL 1 1 FREE ! OVERALL MEAN W FULL 2 1 FREE ! AB AND AW PARAMETERS V FULL 9 1 ! X FULL 9 1 END MATRICES MATRIX A 1 0 1 MATRIX I 1 MATRIX K 2 MATRIX V 1 .5 0 .5 0 -.5 0 -.5 -1 MATRIX X 0 .5 1 -.5 0 .5 -1 -.5 0 SPECIFY F A1S1 A2S1 SPECIFY H A1S2 A2S2 SPECIFY I TYPE BOUND -5 5 B 1 1 BOUND -5 5 N 1 1 BEGIN ALGEBRA; E = I|J|I|K ; ! TO SELECT ROW OF V|X Z = \PART((V|X),E)*W | \PART((V|-X),E)*W ; ! SELECTS ROW OF V|X AND V|-X END ALGEBRA; MEANS (N + (B@U)*F | N + (B@U)*H) + Z; COVARIANCE A*A' ; OPTION ND=4 ! REQUEST 4 DECIMAL PLACES IN OUTPUT OPTION RS MULTIPLE ! REQUEST RESIDUALS, MULTIPLE FIT OPTION ISSAT ! THIS IS SATURATED MODEL FOR SUBMODEL COMPARISON END Summary of VL file data for group 1 TYPE A2S2 A1S2 A2S1 A1S1 P1 P2 Code -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 Mean 4.9580 .5030 .4940 .4970 .4900 -.0415 -.1730 Variance 6.6962 .2500 .2500 .2500 .2499 2.7999 2.7401 Minimum 1.0000 .0000 .0000 .0000 .0000 -5.3776 -6.5806 Maximum 9.0000 1.0000 1.0000 1.0000 1.0000 4.8277 5.6065 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 Simulated data, real allele effect MATRIX A This is a LOWER TRIANGULAR matrix of order 2 by 2 1 2 1 1 2 2 3 MATRIX B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX F This is a FULL matrix of order 2 by 1 1 1 -1 2 -2 MATRIX H This is a FULL matrix of order 2 by 1 1 1 -3 2 -4 MATRIX I This is a FULL matrix of order 1 by 1 1 1 -5 MATRIX J This is a UNIT matrix of order 1 by 1 MATRIX K This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX N This is a FULL matrix of order 1 by 1 1 1 4 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a FULL matrix of order 9 by 1 It has no free parameters specified MATRIX W This is a FULL matrix of order 2 by 1 1 1 5 2 6 MATRIX X This is a FULL matrix of order 9 by 1 It has no free parameters specified MATRIX Z This is a computed FULL matrix of order 1 by 2 It has no free parameters specified MX PARAMETER ESTIMATES GROUP NUMBER: 1 Simulated data, real allele effect MATRIX A This is a LOWER TRIANGULAR matrix of order 2 by 2 1 2 1 1.6065 2 .5359 1.5306 MATRIX B This is a FULL matrix of order 1 by 1 1 1 .0000 MATRIX E This is a computed FULL matrix of order 1 by 4 [=I|J|I|K] 1 2 3 4 1 4.0000 1.0000 4.0000 2.0000 MATRIX F This is a FULL matrix of order 2 by 1 1 1 .0000 2 1.0000 MATRIX H This is a FULL matrix of order 2 by 1 1 1 .0000 2 .0000 MATRIX I This is a FULL matrix of order 1 by 1 1 1 4.0000 MATRIX J This is a UNIT matrix of order 1 by 1 MATRIX K This is a FULL matrix of order 1 by 1 1 1 2.0000 MATRIX N This is a FULL matrix of order 1 by 1 1 1 -.1112 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a FULL matrix of order 9 by 1 1 1 1.0000 2 .5000 3 .0000 4 .5000 5 .0000 6 -.5000 7 .0000 8 -.5000 9 -1.0000 MATRIX W This is a FULL matrix of order 2 by 1 1 1 .6090 2 .4403 MATRIX X This is a FULL matrix of order 9 by 1 1 1 .0000 2 .5000 3 1.0000 4 -.5000 5 .0000 6 .5000 7 -1.0000 8 -.5000 9 .0000 MATRIX Z This is a computed FULL matrix of order 1 by 2 [=\PART((V|X),E)*W|\PART((V|-X),E)*W] 1 2 1 .0843 .5246 Vector of OBSERVED means P1 P2 Mean -.0415 -.1730 Vector of EXPECTED means P1 P2 Mean -.0269 .4134 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX P1 P2 P1 2.5807 P2 .8609 2.6300 Function value of this group: 7475.1831 Where the fit function is -2 * Log-likelihood of raw data Your model has 6 estimated parameters and 2000 Observed statistics -2 times log-likelihood of data >>> 7475.183 Degrees of freedom >>>>>>>>>>>>>>>> 1994 This problem used .9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 2.08 Execution 0: 0: 0:22.35 TOTAL 0: 0: 0:24.43 Total number of warnings issued: 0 ______________________________________________________________________________ Multiple fit option in effect. The following MX script lines have been read: SAVE SET1.MXS EQUATE W 1 1 1 W 1 2 1 END Summary of VL file data for group 1 TYPE A2S2 A1S2 A2S1 A1S1 P1 P2 Code -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 Mean 4.9580 .5030 .4940 .4970 .4900 -.0415 -.1730 Variance 6.6962 .2500 .2500 .2500 .2499 2.7999 2.7401 Minimum 1.0000 .0000 .0000 .0000 .0000 -5.3776 -6.5806 Maximum 9.0000 1.0000 1.0000 1.0000 1.0000 4.8277 5.6065 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 Simulated data, real allele effect MATRIX A This is a LOWER TRIANGULAR matrix of order 2 by 2 1 2 1 1 2 2 3 MATRIX B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX F This is a FULL matrix of order 2 by 1 1 1 -1 2 -2 MATRIX H This is a FULL matrix of order 2 by 1 1 1 -3 2 -4 MATRIX I This is a FULL matrix of order 1 by 1 1 1 -5 MATRIX J This is a UNIT matrix of order 1 by 1 MATRIX K This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX N This is a FULL matrix of order 1 by 1 1 1 4 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a FULL matrix of order 9 by 1 It has no free parameters specified MATRIX W This is a FULL matrix of order 2 by 1 1 1 5 2 5 MATRIX X This is a FULL matrix of order 9 by 1 It has no free parameters specified MATRIX Z This is a computed FULL matrix of order 1 by 2 It has no free parameters specified MX PARAMETER ESTIMATES GROUP NUMBER: 1 Simulated data, real allele effect MATRIX A This is a LOWER TRIANGULAR matrix of order 2 by 2 1 2 1 1.6073 2 .5357 1.5317 MATRIX B This is a FULL matrix of order 1 by 1 1 1 .0000 MATRIX E This is a computed FULL matrix of order 1 by 4 [=I|J|I|K] 1 2 3 4 1 4.0000 1.0000 4.0000 2.0000 MATRIX F This is a FULL matrix of order 2 by 1 1 1 .0000 2 1.0000 MATRIX H This is a FULL matrix of order 2 by 1 1 1 .0000 2 .0000 MATRIX I This is a FULL matrix of order 1 by 1 1 1 4.0000 MATRIX J This is a UNIT matrix of order 1 by 1 MATRIX K This is a FULL matrix of order 1 by 1 1 1 2.0000 MATRIX N This is a FULL matrix of order 1 by 1 1 1 -.1107 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a FULL matrix of order 9 by 1 1 1 1.0000 2 .5000 3 .0000 4 .5000 5 .0000 6 -.5000 7 .0000 8 -.5000 9 -1.0000 MATRIX W This is a FULL matrix of order 2 by 1 1 1 .5453 2 .5453 MATRIX X This is a FULL matrix of order 9 by 1 1 1 .0000 2 .5000 3 1.0000 4 -.5000 5 .0000 6 .5000 7 -1.0000 8 -.5000 9 .0000 MATRIX Z This is a computed FULL matrix of order 1 by 2 [=\PART((V|X),E)*W|\PART((V|-X),E)*W] 1 2 1 .0000 .5453 Vector of OBSERVED means P1 P2 Mean -.0415 -.1730 Vector of EXPECTED means P1 P2 Mean -.1107 .4346 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX P1 P2 P1 2.5835 P2 .8611 2.6330 Function value of this group: 7477.6276 Where the fit function is -2 * Log-likelihood of raw data Your model has 5 estimated parameters and 2000 Observed statistics -2 times log-likelihood of data >>> 7477.628 Degrees of freedom >>>>>>>>>>>>>>>> 1995 Saturated model fit* >>>>>>>>>>> 7475.183 Saturated model df* >>>>>>>>>>> 1994 Difference Chi-squared >>>>>>>> 2.445 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> .118 Akaike's Information Criterion > .445 * Saturated model statistic computed earlier in this job This problem used .9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: .65 Execution 0: 0: 0:13.58 TOTAL 0: 0: 0:14.23 Total number of warnings issued: 0 ______________________________________________________________________________ Multiple fit option in effect. The following MX script lines have been read: DROP W 1 1 1 END Summary of VL file data for group 1 TYPE A2S2 A1S2 A2S1 A1S1 P1 P2 Code -5.0000 -4.0000 -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 1000.0000 Mean 4.9580 .5030 .4940 .4970 .4900 -.0415 -.1730 Variance 6.6962 .2500 .2500 .2500 .2499 2.7999 2.7401 Minimum 1.0000 .0000 .0000 .0000 .0000 -5.3776 -6.5806 Maximum 9.0000 1.0000 1.0000 1.0000 1.0000 4.8277 5.6065 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 Simulated data, real allele effect MATRIX A This is a LOWER TRIANGULAR matrix of order 2 by 2 1 2 1 1 2 2 3 MATRIX B This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX E This is a computed FULL matrix of order 1 by 4 It has no free parameters specified MATRIX F This is a FULL matrix of order 2 by 1 1 1 -1 2 -2 MATRIX H This is a FULL matrix of order 2 by 1 1 1 -3 2 -4 MATRIX I This is a FULL matrix of order 1 by 1 1 1 -5 MATRIX J This is a UNIT matrix of order 1 by 1 MATRIX K This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX N This is a FULL matrix of order 1 by 1 1 1 4 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a FULL matrix of order 9 by 1 It has no free parameters specified MATRIX W This is a FULL matrix of order 2 by 1 It has no free parameters specified MATRIX X This is a FULL matrix of order 9 by 1 It has no free parameters specified MATRIX Z This is a computed FULL matrix of order 1 by 2 It has no free parameters specified MX PARAMETER ESTIMATES GROUP NUMBER: 1 Simulated data, real allele effect MATRIX A This is a LOWER TRIANGULAR matrix of order 2 by 2 1 2 1 1.6746 2 .5872 1.5490 MATRIX B This is a FULL matrix of order 1 by 1 1 1 .0000 MATRIX E This is a computed FULL matrix of order 1 by 4 [=I|J|I|K] 1 2 3 4 1 4.0000 1.0000 4.0000 2.0000 MATRIX F This is a FULL matrix of order 2 by 1 1 1 .0000 2 1.0000 MATRIX H This is a FULL matrix of order 2 by 1 1 1 .0000 2 .0000 MATRIX I This is a FULL matrix of order 1 by 1 1 1 4.0000 MATRIX J This is a UNIT matrix of order 1 by 1 MATRIX K This is a FULL matrix of order 1 by 1 1 1 2.0000 MATRIX N This is a FULL matrix of order 1 by 1 1 1 -.1084 MATRIX U This is a UNIT matrix of order 1 by 2 MATRIX V This is a FULL matrix of order 9 by 1 1 1 1.0000 2 .5000 3 .0000 4 .5000 5 .0000 6 -.5000 7 .0000 8 -.5000 9 -1.0000 MATRIX W This is a FULL matrix of order 2 by 1 1 1 .0000 2 .0000 MATRIX X This is a FULL matrix of order 9 by 1 1 1 .0000 2 .5000 3 1.0000 4 -.5000 5 .0000 6 .5000 7 -1.0000 8 -.5000 9 .0000 MATRIX Z This is a computed FULL matrix of order 1 by 2 [=\PART((V|X),E)*W|\PART((V|-X),E)*W] 1 2 1 .0000 .0000 Vector of OBSERVED means P1 P2 Mean -.0415 -.1730 Vector of EXPECTED means P1 P2 Mean -.1084 -.1084 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX P1 P2 P1 2.8044 P2 .9834 2.7442 Function value of this group: 7582.1661 Where the fit function is -2 * Log-likelihood of raw data Your model has 4 estimated parameters and 2000 Observed statistics -2 times log-likelihood of data >>> 7582.166 Degrees of freedom >>>>>>>>>>>>>>>> 1996 Saturated model fit* >>>>>>>>>>> 7475.183 Saturated model df* >>>>>>>>>>> 1994 Difference Chi-squared >>>>>>>> 106.983 Difference d.f. >>>>>>>>>>>>>>> 2 Probability >>>>>>>>>>>>>>>>>>>> .000 Akaike's Information Criterion > 102.983 * Saturated model statistic computed earlier in this job This problem used .9% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: .00 Execution 0: 0: 0: 8.48 TOTAL 0: 0: 0: 8.48 Total number of warnings issued: 0 ______________________________________________________________________________ ______________________________________________________________________________