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