**MX-PC 1.65b** Job started on 03/05/07 at 14:08:46 ! ESTIMATE GENETIC (QTL) AND ENVIRONMENTAL COMPONENTS - FEQ MODEL - PIHAT APPROACH ! BRISBANE TWIN AND FAMILY STUDY OF COGNITION #DEFINE NVAR 1 The following MX script lines were read for group 1 #NGROUPS 1 Note: #NGroup set number of groups to 1 DZ / SIBS GENOTYPED DATA NINPUT=182 MAXREC=1500 RECTANGULAR FILE=PIQIBD.REC Rectangular continuous data read initiated Note: Maximum ordinal/rectangular record length is: 1500 NOTE: Rectangular file contained 710 records with data that contained a total of 128656 observations LABELS FAM ID1 ID2 PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 IBD0M2 IBD1M2 IBD2M2 IBD0M3 IBD1M3 IBD2M3 IBD0M4 IBD1M4 IBD2M4 IBD0M5 IBD1M5 IBD2M5 IBD0M6 IBD1M6 IBD2M6 IBD0M7 IBD1M7 IBD2M7 IBD0M8 IBD1M8 IBD2M8 IBD0M9 IBD1M9 IBD2M9 IBD0M10 IBD1M10 IBD2M10 IBD0M11 IBD1M11 IBD2M11 IBD0M12 IBD1M12 IBD2M12 IBD0M13 IBD1M13 IBD2M13 IBD0M14 IBD1M14 IBD2M14 IBD0M15 IBD1M15 IBD2M15 IBD0M16 IBD1M16 IBD2M16 IBD0M17 IBD1M17 IBD2M17 IBD0M18 IBD1M18 IBD2M18 IBD0M19 IBD1M19 IBD2M19 IBD0M20 IBD1M20 IBD2M20 IBD0M21 IBD1M21 IBD2M21 IBD0M22 IBD1M22 IBD2M22 IBD0M23 IBD1M23 IBD2M23 IBD0M24 IBD1M24 IBD2M24 IBD0M25 IBD1M25 IBD2M25 IBD0M26 IBD1M26 IBD2M26 IBD0M27 IBD1M27 IBD2M27 IBD0M28 IBD1M28 IBD2M28 IBD0M29 IBD1M29 IBD2M29 IBD0M30 IBD1M30 IBD2M30 IBD0M31 IBD1M31 IBD2M31 IBD0M32 IBD1M32 IBD2M32 IBD0M33 IBD1M33 IBD2M33 IBD0M34 IBD1M34 IBD2M34 IBD0M35 IBD1M35 IBD2M35 IBD0M36 IBD1M36 IBD2M36 IBD0M37 IBD1M37 IBD2M37 IBD0M38 IBD1M38 IBD2M38 IBD0M39 IBD1M39 IBD2M39 IBD0M40 IBD1M40 IBD2M40 IBD0M41 IBD1M41 IBD2M41 IBD0M42 IBD1M42 IBD2M42 IBD0M43 IBD1M43 IBD2M43 IBD0M44 IBD1M44 IBD2M44 IBD0M45 IBD1M45 IBD2M45 IBD0M46 IBD1M46 IBD2M46 IBD0M47 IBD1M47 IBD2M47 IBD0M48 IBD1M48 IBD2M48 IBD0M49 IBD1M49 IBD2M49 IBD0M50 IBD1M50 IBD2M50 IBD0M51 IBD1M51 IBD2M51 IBD0M52 IBD1M52 IBD2M52 IBD0M53 IBD1M53 IBD2M53 IBD0M54 IBD1M54 IBD2M54 IBD0M55 IBD1M55 IBD2M55 IBD0M56 IBD1M56 IBD2M56 IBD0M57 IBD1M57 IBD2M57 IBD0M58 IBD1M58 IBD2M58 IBD0M59 IBD1M59 IBD2M59 SELECT PIQ1 PIQ2 IBD0M1 IBD1M1 IBD2M1 ; DEFINITION IBD0M1 IBD1M1 IBD2M1 ; NOTE: Selection yields 710 data vectors for analysis NOTE: Vectors contain a total of 2986 observations NOTE: Definition yields 550 data vectors for analysis NOTE: Vectors contain a total of 856 observations BEGIN MATRICES; X LOWER NVAR NVAR FREE ! RESIDUAL FAMILIAL F Z LOWER NVAR NVAR FREE ! UNSHARED ENVIRONMENT E L FULL NVAR 1 FREE ! QTL EFFECT Q G FULL 1 NVAR FREE ! GRAND MEANS H FULL 1 1 ! SCALAR, .5 K FULL 3 1 ! IBD PROBABILITIES (FROM MERLIN) J FULL 1 3 ! COEFFICIENTS 0.5,1 FOR PIHAT END MATRICES; SPECIFY K IBD0M1 IBD1M1 IBD2M1 ; MATRIX H .5 MATRIX J 0 .5 1 START 5 X 1 1 1 START 5 L 1 1 1 START 6 Z 1 1 1 START 111 G 1 1 1 BEGIN ALGEBRA; F= X*X'; ! RESIDUAL FAMILIAL VARIANCE E= Z*Z'; ! UNIQUE ENVIRONMENTAL VARIANCE Q= L*L'; ! VARIANCE DUE TO QTL V= F+Q+E; ! TOTAL VARIANCE T= F|Q|E; ! PARAMETERS IN ONE MATRIX S= F%V| Q%V| E%V; ! STANDARDIZED VARIANCE COMPONENT ESTIMATES P= J*K; ! ESTIMATE OF PIHAT END ALGEBRA; LABELS ROW S STANDEST LABELS COL S F^2 Q^2 E^2 LABELS ROW T UNSTANDEST LABELS COL T F^2 Q^2 E^2 MEANS G| G ; COVARIANCE F+E+Q | F+P@Q_ F+P@Q | F+E+Q ; OPTION RSIDUALS NDECIMALS=4 OPTION MULTIPLE ISSAT END Summary of VL file data for group 1 IBD2M1 IBD1M1 IBD0M1 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2415 0.5058 0.2527 111.9452 111.5210 Variance 0.1157 0.1099 0.0965 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9787 0.9954 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS genotyped MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 1 1 3 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 4 MX PARAMETER ESTIMATES GROUP NUMBER: 1 DZ / SIBS genotyped MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0679 2 0.3746 3 0.5575 MATRIX L This is a FULL matrix of order 1 by 1 1 1 -0.0001 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.7448 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data Your model has 4 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 852 Akaike's Information Criterion >>>> 5499.350 Bayesian Information Criterion >>>> 913.650 Sample size Adjusted BIC >>>> 2265.955 Deviance Information Criterion >>>> 1696.586 This problem used 13.1% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.47 Execution 0: 0: 0: 2.98 TOTAL 0: 0: 0: 3.45 Total number of warnings issued: 0 ______________________________________________________________________________ ! TEST SIGNIFICANCE OF QTL EFFECT Multiple fit option in effect. The following MX script lines have been read: DROP L 1 1 1 EXIT Summary of VL file data for group 1 IBD2M1 IBD1M1 IBD0M1 PIQ1 PIQ2 Code -3.0000 -2.0000 -1.0000 1.0000 2.0000 Number 550.0000 550.0000 550.0000 547.0000 309.0000 Mean 0.2415 0.5058 0.2527 111.9452 111.5210 Variance 0.1157 0.1099 0.0965 271.9751 281.1169 Minimum 0.0000 0.0000 0.0000 68.0000 68.0000 Maximum 0.9787 0.9954 1.0000 149.0000 150.0000 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 DZ / SIBS genotyped MATRIX E This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX F This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX G This is a FULL matrix of order 1 by 1 1 1 4 MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX J This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX L This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX 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 3 It has no free parameters specified MATRIX T This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX V This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 Mx starting optimization; number of parameters = 3 *** 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 DZ / SIBS genotyped MATRIX E This is a computed FULL matrix of order 1 by 1 [=Z*Z'] 1 1 183.9281 MATRIX F This is a computed FULL matrix of order 1 by 1 [=X*X'] 1 1 91.7447 MATRIX G This is a FULL matrix of order 1 by 1 1 1 111.7834 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.5000 MATRIX J This is a FULL matrix of order 1 by 3 1 2 3 1 0.0000 0.5000 1.0000 MATRIX K This is a FULL matrix of order 3 by 1 1 1 0.0679 2 0.3746 3 0.5575 MATRIX L This is a FULL matrix of order 1 by 1 1 1 0.0000 MATRIX P This is a computed FULL matrix of order 1 by 1 [=J*K] 1 1 0.7448 MATRIX Q This is a computed FULL matrix of order 1 by 1 [=L*L'] 1 1 0.0000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=F%V|Q%V|E%V] F^2 Q^2 E^2 STANDEST 0.3328 0.0000 0.6672 MATRIX T This is a computed FULL matrix of order 1 by 3 [=F|Q|E] F^2 Q^2 E^2 UNSTANDEST 91.7447 0.0000 183.9281 MATRIX V This is a computed FULL matrix of order 1 by 1 [=F+Q+E] 1 1 275.6728 MATRIX X This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 9.5783 MATRIX Z This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 13.5620 Vector of OBSERVED means PIQ1 PIQ2 Mean 111.9452 111.5210 Vector of EXPECTED means PIQ1 PIQ2 Mean 111.7834 111.7834 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX PIQ1 PIQ2 PIQ1 275.6728 PIQ2 91.7447 275.6728 Function value of this group: 7203.3503 Where the fit function is -2 * Log-likelihood of raw data *** WARNING! *** Minimization may not be successful. See above CODE GREEN - it probably was OK Your model has 3 estimated parameters and 856 Observed statistics -2 times log-likelihood of data >>> 7203.350 Degrees of freedom >>>>>>>>>>>>>>>> 853 Akaike's Information Criterion >>>> 5497.350 Bayesian Information Criterion >>>> 910.495 Sample size Adjusted BIC >>>> 2264.387 Deviance Information Criterion >>>> 1694.350 Saturated model fit* >>>>>>>>>>> 7203.350 Saturated model df* >>>>>>>>>>> 852 Difference Chi-squared >>>>>>>> 0.000 Difference d.f. >>>>>>>>>>>>>>> 1 Probability incalculable Akaike's Information Criterion > -2.000 * Saturated model statistic computed earlier in this job This problem used 13.1% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 0.17 TOTAL 0: 0: 0: 0.17 Total number of warnings issued: 2 ______________________________________________________________________________