** Mx startup successful ** **MX-PC 1.46b** Job started on 03/17/00 at 13:08:40 ! ! This is a univariate linkage job, courtesy of D. Boomsma, March 2000 ! ! The data are from Keavney et al. (HMG, 1999) on angiotensin- ! converting enzyme (ace). This script reads in some family identifiers, ! then the probability of sharing 0, 1, or 2 alleles ibd (pibd0, pibd1, pibd2), ! followed by the first sib's genotype (a1s1,a2s1) then the second sib's ! genotype (a1s2,a2s2). Note that the ibd sharing probabilities can be obtained ! from, e.g., Mapmaker/Sibs, Genehunter or Simwalk2. ! The following MX script lines were read for group 1 #DEFINE NVAR 1 TITLE QTL LINKAGE MODEL DATA NGROUPS=1 NINPUT=13 NMODEL=1 MISSING=-99.989998 NOTE: Missing value *string* set to '-99.989998' RECTANGULAR FILE=MARKER10.DAT NOTE: Rectangular file contained 107 records with data LABELS LOCUS PEDNUM ID1 ID2 PIBD0 PIBD1 PIBD2 ACE1 ACE2 A1S1 A2S1 A1S2 A2S2 SELECT IF A1S1 ^= 0 ! THESE REPRESENT A POOR-MAN'S MISSING VALUE CODES NOTE: Select if yields 105 data vectors for analysis NOTE: Vectors contain a total of 1357 observations SELECT IF A2S1 ^= 0 ! THE GENOTYPES ARE CODED AS 11, 12 AND 22 NOTE: Select if yields 105 data vectors for analysis NOTE: Vectors contain a total of 1357 observations SELECT IF A1S2 ^= 0 ! FOR MARKER ALLELES AA, AA, AND AA NOTE: Select if yields 104 data vectors for analysis NOTE: Vectors contain a total of 1344 observations SELECT IF A2S2 ^= 0 ! NOTE: Select if yields 104 data vectors for analysis NOTE: Vectors contain a total of 1344 observations SELECT PIBD0 PIBD1 PIBD2 ACE1 ACE2 /! WE DON'T NEED THE GENOTYPES FOR LINKAGE DEFINITION PIBD0 PIBD1 PIBD2/ NOTE: Selection yields 104 data vectors for analysis NOTE: Vectors contain a total of 512 observations MATRICES NOTE: Definition yields 103 data vectors for analysis NOTE: Vectors contain a total of 200 observations A LOWER NVAR NVAR FREE !GENETIC BACKGROUND (PLUS C, AGE, ETC) E LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENT Q FULL NVAR 1 FREE !QTL EFFECT M FULL 1 NVAR FREE !MEANS K FULL 3 1 !IBD PROBABILITIES (FROM MAPMAKER/SIBS) GO HERE F FULL 1 3 FIXED !CONTAINS THE COEFFICIENTS 0,0.5,1 TO CREATE PIHAT H FULL 1 1 END MATRICES MATRIX F 0. 0.5 1.0 MATRIX H .5 SPECIFY K PIBD0 PIBD1 PIBD2; BEGIN ALGEBRA; P = F*K; !ESTIMATE OF PI U = H@A*A' ; !BACKGROUND GENETIC COVARIANCE W = U + P@Q*Q' ; !TOTAL GENETIC COVARIANCE V = A*A' + Q*Q' + E*E'; !TOTAL VARIANCE Z = A*A' | Q*Q' | E*E'; !PUT PARAMETERS IN ONE MATRIX FOR STANDARDIZING; S = Z@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES Y = V|W_ !EXPECTED PHENOTYPIC MATRIX W|V; END ALGEBRA; LABELS ROW S STANDEST LABELS COL S A^2 Q^2 E^2 LABELS ROW Z RAWEST LABELS COL Z A^2 Q^2 E^2 MEANS M |M ; COVARIANCE Y ; MATRIX A .71 !START VALUES MATRIX E .5 MATRIX Q .5 MATRIX M 0.0 BOUND .001 100 E 1 1 OPTION RS ND=3 OPTION IT=5000 OPTION MULTIPLE OPTION ISSAT END Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 ACE1 ACE2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 103.000 103.000 103.000 97.000 103.000 Mean 0.352 0.431 0.216 -0.043 -0.015 Variance 0.164 0.115 0.092 1.021 1.100 Minimum 0.000 0.000 0.000 -2.026 -2.109 Maximum 1.000 1.000 1.000 3.027 2.670 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 Title QTL linkage model MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX E This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX F This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a FULL matrix of order 1 by 1 1 1 3 MATRIX S This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MATRIX U This is a computed FULL matrix of order 1 by 1 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 computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Y This is a computed FULL matrix of order 2 by 2 It has no free parameters specified MATRIX Z This is a computed FULL matrix of order 1 by 3 It has no free parameters specified *** 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 Title QTL linkage model MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.000 MATRIX E This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.486 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 1.000 2 0.000 3 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 -0.016 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.000 MATRIX Q This is a FULL matrix of order 1 by 1 1 1 0.905 MATRIX S This is a computed FULL matrix of order 1 by 3 [=Z@V~] A^2 Q^2 E^2 STANDEST 0.000 0.776 0.224 MATRIX U This is a computed FULL matrix of order 1 by 1 [=H@A*A'] 1 1 0.000 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A*A'+Q*Q'+E*E'] 1 1 1.056 MATRIX W This is a computed FULL matrix of order 1 by 1 [=U+P@Q*Q'] 1 1 0.000 MATRIX Y This is a computed FULL matrix of order 2 by 2 [=V|W_W|V] 1 2 1 1.056 0.000 2 0.000 1.056 MATRIX Z This is a computed FULL matrix of order 1 by 3 [=A*A'|Q*Q'|E*E'] A^2 Q^2 E^2 RAWEST 0.000 0.820 0.236 Vector of OBSERVED means ACE1 ACE2 Mean 0.000 0.000 Vector of EXPECTED means ACE1 ACE2 Mean -0.016 -0.016 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 1.056 ACE2 0.000 1.056 Function value of this group: 545.182 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 4 estimated parameters and 509 Observed statistics -2 times log-likelihood of data >>> 545.182 Degrees of freedom >>>>>>>>>>>>>>>> 505 This problem used 3.8% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.77 Execution 0: 0: 0: 8.24 TOTAL 0: 0: 0: 9.01 Total number of warnings issued: 2 ______________________________________________________________________________ Multiple fit option in effect. The following MX script lines have been read: DROP @.0 3 END Summary of VL file data for group 1 PIBD2 PIBD1 PIBD0 ACE1 ACE2 Code -3.000 -2.000 -1.000 1.000 2.000 Number 103.000 103.000 103.000 97.000 103.000 Mean 0.352 0.431 0.216 -0.043 -0.015 Variance 0.164 0.115 0.092 1.021 1.100 Minimum 0.000 0.000 0.000 -2.026 -2.109 Maximum 1.000 1.000 1.000 3.027 2.670 PARAMETER SPECIFICATIONS GROUP NUMBER: 1 Title QTL linkage model MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 1 MATRIX E This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 2 MATRIX F This is a FULL matrix of order 1 by 3 It has no free parameters specified MATRIX H This is a FULL matrix of order 1 by 1 It has no free parameters specified MATRIX K This is a FULL matrix of order 3 by 1 1 1 -1 2 -2 3 -3 MATRIX M This is a FULL matrix of order 1 by 1 1 1 4 MATRIX P This is a computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Q This is a 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 U This is a computed FULL matrix of order 1 by 1 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 computed FULL matrix of order 1 by 1 It has no free parameters specified MATRIX Y This is a computed FULL matrix of order 2 by 2 It has no free parameters specified MATRIX Z This is a computed FULL matrix of order 1 by 3 It has no free parameters specified MX PARAMETER ESTIMATES GROUP NUMBER: 1 Title QTL linkage model MATRIX A This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 -0.922 MATRIX E This is a LOWER TRIANGULAR matrix of order 1 by 1 1 1 0.459 MATRIX F This is a FULL matrix of order 1 by 3 1 2 3 1 0.000 0.500 1.000 MATRIX H This is a FULL matrix of order 1 by 1 1 1 0.500 MATRIX K This is a FULL matrix of order 3 by 1 1 1 1.000 2 0.000 3 0.000 MATRIX M This is a FULL matrix of order 1 by 1 1 1 -0.030 MATRIX P This is a computed FULL matrix of order 1 by 1 [=F*K] 1 1 0.000 MATRIX Q This is a FULL matrix of order 1 by 1 1 1 0.000 MATRIX S This is a computed FULL matrix of order 1 by 3 [=Z@V~] A^2 Q^2 E^2 STANDEST 0.801 0.000 0.199 MATRIX U This is a computed FULL matrix of order 1 by 1 [=H@A*A'] 1 1 0.425 MATRIX V This is a computed FULL matrix of order 1 by 1 [=A*A'+Q*Q'+E*E'] 1 1 1.061 MATRIX W This is a computed FULL matrix of order 1 by 1 [=U+P@Q*Q'] 1 1 0.425 MATRIX Y This is a computed FULL matrix of order 2 by 2 [=V|W_W|V] 1 2 1 1.061 0.425 2 0.425 1.061 MATRIX Z This is a computed FULL matrix of order 1 by 3 [=A*A'|Q*Q'|E*E'] A^2 Q^2 E^2 RAWEST 0.850 0.000 0.211 Vector of OBSERVED means ACE1 ACE2 Mean 0.000 0.000 Vector of EXPECTED means ACE1 ACE2 Mean -0.030 -0.030 (OBSERVED MATRIX is nonexistent for raw data) EXPECTED COVARIANCE MATRIX ACE1 ACE2 ACE1 1.061 ACE2 0.425 1.061 Function value of this group: 562.409 Where the fit function is -2 * Log-likelihood of raw data Your model has 3 estimated parameters and 509 Observed statistics -2 times log-likelihood of data >>> 562.409 Degrees of freedom >>>>>>>>>>>>>>>> 506 Saturated model fit* >>>>>>>>>>> 545.182 Saturated model df* >>>>>>>>>>> 505 Difference Chi-squared >>>>>>>> 17.228 Difference d.f. >>>>>>>>>>>>>>> 1 Probability >>>>>>>>>>>>>>>>>>>> 0.000 Akaike's Information Criterion > 15.228 * Saturated model statistic computed earlier in this job This problem used 3.8% of my workspace Task Time elapsed (DD:HH:MM:SS) Reading script & data 0: 0: 0: 0.00 Execution 0: 0: 0: 7.30 TOTAL 0: 0: 0: 7.30 Total number of warnings issued: 2 ______________________________________________________________________________