** Mx startup successful **
**MX-PC 1.54** Job started on 03/04/03 at 14:36:00
!QTL analysis via Pihat method
!Using marker1
!Using MZ and DZ twins
!Analysis of LDL
!Dutch Adults
#repeat 54
Note: beginning of #Repeat section
The following MX script lines were read for group 1
#DEFINE NVAR 1
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1284 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 183 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF1
Note: Opening #include file 1 seldef1
SELECT IBD0M1 IBD1M1 IBD2M1 LDL1 LDL2;
DEFINITION IBD0M1 IBD1M1 IBD2M1;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY1
Note: Opening #include file 1 specify1
SPECIFY K IBD0M1 IBD1M1 IBD2M1
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 91.000 92.000
Mean 3.688 3.719
Variance 0.964 0.749
Minimum 1.660 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M1 IBD1M1 IBD0M1 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.259 0.501 0.240 3.558 3.632
Variance 0.047 0.020 0.032 1.012 1.164
Minimum 0.027 0.275 0.035 0.000 0.000
Maximum 0.659 0.722 0.697 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.818
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.195
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.635
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 C^2 Q^2 E^2
STANDEST 0.807 0.000 0.000 0.193
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.818 0.000 0.000 0.195
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.013
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.904
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.442
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.818
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.195
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.635
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 C^2 Q^2 E^2
STANDEST 0.807 0.000 0.000 0.193
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.818 0.000 0.000 0.195
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.013
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.904
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.442
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.818
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.195
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.325
2 0.574
3 0.101
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 3.635
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.388
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 C^2 Q^2 E^2
STANDEST 0.807 0.000 0.000 0.193
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.818 0.000 0.000 0.195
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.013
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.904
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.442
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 417 Observed statistics
-2 times log-likelihood of data >>> 1072.153
Degrees of freedom >>>>>>>>>>>>>>>> 412
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.03
Execution 0: 0: 0:-0.03
TOTAL 0: 0: 0: 2.00
Total number of warnings issued: 2
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 91.000 92.000
Mean 3.688 3.719
Variance 0.964 0.749
Minimum 1.660 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M1 IBD1M1 IBD0M1 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.259 0.501 0.240 3.558 3.632
Variance 0.047 0.020 0.032 1.012 1.164
Minimum 0.027 0.275 0.035 0.000 0.000
Maximum 0.659 0.722 0.697 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.818
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.195
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.635
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 C^2 Q^2 E^2
STANDEST 0.807 0.000 0.000 0.193
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.818 0.000 0.000 0.195
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.013
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.904
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.442
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.818
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.195
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.635
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 C^2 Q^2 E^2
STANDEST 0.807 0.000 0.000 0.193
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.818 0.000 0.000 0.195
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.013
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.904
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.442
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.818
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.195
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.325
2 0.574
3 0.101
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 3.635
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.388
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 C^2 Q^2 E^2
STANDEST 0.807 0.000 0.000 0.193
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.818 0.000 0.000 0.195
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.013
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.904
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.442
Your model has 4 estimated parameters and 417 Observed statistics
-2 times log-likelihood of data >>> 1072.153
Degrees of freedom >>>>>>>>>>>>>>>> 413
Saturated model fit* >>>>>>>>>>> 1072.153
Saturated model df* >>>>>>>>>>> 412
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.55
TOTAL 0: 0: 0: 0.55
Total number of warnings issued: 2
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF2
Note: Opening #include file 1 seldef2
SELECT IBD0M2 IBD1M2 IBD2M2 LDL1 LDL2;
DEFINITION IBD0M2 IBD1M2 IBD2M2;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY2
Note: Opening #include file 1 specify2
SPECIFY K IBD0M2 IBD1M2 IBD2M2
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M2 IBD1M2 IBD0M2 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.260 0.501 0.239 3.558 3.632
Variance 0.057 0.028 0.038 1.012 1.164
Minimum 0.019 0.236 0.026 0.000 0.000
Maximum 0.702 0.761 0.745 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.328
2 0.587
3 0.085
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.378
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.19
Execution 0: 0: 0:-0.40
TOTAL 0: 0: 0: 1.79
Total number of warnings issued: 4
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M2 IBD1M2 IBD0M2 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.260 0.501 0.239 3.558 3.632
Variance 0.057 0.028 0.038 1.012 1.164
Minimum 0.019 0.236 0.026 0.000 0.000
Maximum 0.702 0.761 0.745 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.328
2 0.587
3 0.085
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.378
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.01
Execution 0: 0: 0: 0.12
TOTAL 0: 0: 0: 0.13
Total number of warnings issued: 4
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF3
Note: Opening #include file 1 seldef3
SELECT IBD0M3 IBD1M3 IBD2M3 LDL1 LDL2;
DEFINITION IBD0M3 IBD1M3 IBD2M3;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY3
Note: Opening #include file 1 specify3
SPECIFY K IBD0M3 IBD1M3 IBD2M3
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M3 IBD1M3 IBD0M3 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.261 0.501 0.238 3.558 3.632
Variance 0.069 0.038 0.045 1.012 1.164
Minimum 0.011 0.191 0.018 0.000 0.000
Maximum 0.750 0.806 0.798 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.331
2 0.602
3 0.067
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.368
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.89
Execution 0: 0: 0:-0.59
TOTAL 0: 0: 0: 1.30
Total number of warnings issued: 6
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M3 IBD1M3 IBD0M3 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.261 0.501 0.238 3.558 3.632
Variance 0.069 0.038 0.045 1.012 1.164
Minimum 0.011 0.191 0.018 0.000 0.000
Maximum 0.750 0.806 0.798 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.331
2 0.602
3 0.067
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.368
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.14
TOTAL 0: 0: 0: 0.14
Total number of warnings issued: 6
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF4
Note: Opening #include file 1 seldef4
SELECT IBD0M4 IBD1M4 IBD2M4 LDL1 LDL2;
DEFINITION IBD0M4 IBD1M4 IBD2M4;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY4
Note: Opening #include file 1 specify4
SPECIFY K IBD0M4 IBD1M4 IBD2M4
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M4 IBD1M4 IBD0M4 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.262 0.501 0.237 3.558 3.632
Variance 0.084 0.053 0.054 1.012 1.164
Minimum 0.005 0.137 0.011 0.000 0.000
Maximum 0.804 0.859 0.858 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.333
2 0.620
3 0.047
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.357
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.98
Execution 0: 0: 0:-0.67
TOTAL 0: 0: 0: 1.31
Total number of warnings issued: 6
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M4 IBD1M4 IBD0M4 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.262 0.501 0.237 3.558 3.632
Variance 0.084 0.053 0.054 1.012 1.164
Minimum 0.005 0.137 0.011 0.000 0.000
Maximum 0.804 0.859 0.858 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.333
2 0.620
3 0.047
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.357
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.13
TOTAL 0: 0: 0: 0.13
Total number of warnings issued: 6
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF5
Note: Opening #include file 1 seldef5
SELECT IBD0M5 IBD1M5 IBD2M5 LDL1 LDL2;
DEFINITION IBD0M5 IBD1M5 IBD2M5;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY5
Note: Opening #include file 1 specify5
SPECIFY K IBD0M5 IBD1M5 IBD2M5
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M5 IBD1M5 IBD0M5 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.263 0.501 0.236 3.558 3.632
Variance 0.103 0.073 0.064 1.012 1.164
Minimum 0.001 0.074 0.005 0.000 0.000
Maximum 0.864 0.922 0.925 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.335
2 0.640
3 0.025
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.345
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.40
Execution 0: 0: 0:-1.11
TOTAL 0: 0: 0: 1.29
Total number of warnings issued: 6
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M5 IBD1M5 IBD0M5 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.263 0.501 0.236 3.558 3.632
Variance 0.103 0.073 0.064 1.012 1.164
Minimum 0.001 0.074 0.005 0.000 0.000
Maximum 0.864 0.922 0.925 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.335
2 0.640
3 0.025
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.345
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.14
TOTAL 0: 0: 0: 0.14
Total number of warnings issued: 6
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF6
Note: Opening #include file 1 seldef6
SELECT IBD0M6 IBD1M6 IBD2M6 LDL1 LDL2;
DEFINITION IBD0M6 IBD1M6 IBD2M6;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY6
Note: Opening #include file 1 specify6
SPECIFY K IBD0M6 IBD1M6 IBD2M6
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M6 IBD1M6 IBD0M6 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.264 0.501 0.235 3.558 3.632
Variance 0.127 0.100 0.077 1.012 1.164
Minimum 0.000 0.000 0.001 0.000 0.000
Maximum 0.932 0.995 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.335
2 0.665
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.332
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.93
Execution 0: 0: 0:-0.27
TOTAL 0: 0: 0: 1.66
Total number of warnings issued: 6
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M6 IBD1M6 IBD0M6 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.264 0.501 0.235 3.558 3.632
Variance 0.127 0.100 0.077 1.012 1.164
Minimum 0.000 0.000 0.001 0.000 0.000
Maximum 0.932 0.995 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.335
2 0.665
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.332
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.15
TOTAL 0: 0: 0: 0.15
Total number of warnings issued: 6
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF7
Note: Opening #include file 1 seldef7
SELECT IBD0M7 IBD1M7 IBD2M7 LDL1 LDL2;
DEFINITION IBD0M7 IBD1M7 IBD2M7;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY7
Note: Opening #include file 1 specify7
SPECIFY K IBD0M7 IBD1M7 IBD2M7
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M7 IBD1M7 IBD0M7 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.264 0.499 0.238 3.558 3.632
Variance 0.114 0.081 0.069 1.012 1.164
Minimum 0.000 0.028 0.001 0.000 0.000
Maximum 0.925 0.945 0.972 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.365
2 0.628
3 0.007
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.321
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.92
Execution 0: 0: 0:-0.64
TOTAL 0: 0: 0: 1.28
Total number of warnings issued: 6
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M7 IBD1M7 IBD0M7 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.264 0.499 0.238 3.558 3.632
Variance 0.114 0.081 0.069 1.012 1.164
Minimum 0.000 0.028 0.001 0.000 0.000
Maximum 0.925 0.945 0.972 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.365
2 0.628
3 0.007
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.321
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.13
TOTAL 0: 0: 0: 0.13
Total number of warnings issued: 6
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF8
Note: Opening #include file 1 seldef8
SELECT IBD0M8 IBD1M8 IBD2M8 LDL1 LDL2;
DEFINITION IBD0M8 IBD1M8 IBD2M8;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY8
Note: Opening #include file 1 specify8
SPECIFY K IBD0M8 IBD1M8 IBD2M8
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M8 IBD1M8 IBD0M8 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.263 0.495 0.241 3.558 3.632
Variance 0.107 0.071 0.067 1.012 1.164
Minimum 0.000 0.050 0.002 0.000 0.000
Maximum 0.924 0.920 0.950 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.392
2 0.596
3 0.011
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.309
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.92
Execution 0: 0: 0:-0.55
TOTAL 0: 0: 0: 1.37
Total number of warnings issued: 8
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M8 IBD1M8 IBD0M8 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.263 0.495 0.241 3.558 3.632
Variance 0.107 0.071 0.067 1.012 1.164
Minimum 0.000 0.050 0.002 0.000 0.000
Maximum 0.924 0.920 0.950 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.392
2 0.596
3 0.011
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.309
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.14
TOTAL 0: 0: 0: 0.14
Total number of warnings issued: 8
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF9
Note: Opening #include file 1 seldef9
SELECT IBD0M9 IBD1M9 IBD2M9 LDL1 LDL2;
DEFINITION IBD0M9 IBD1M9 IBD2M9;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY9
Note: Opening #include file 1 specify9
SPECIFY K IBD0M9 IBD1M9 IBD2M9
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M9 IBD1M9 IBD0M9 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.264 0.491 0.245 3.558 3.632
Variance 0.107 0.070 0.069 1.012 1.164
Minimum 0.001 0.066 0.001 0.000 0.000
Maximum 0.932 0.906 0.934 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.419
2 0.569
3 0.011
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.296
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.99
Execution 0: 0: 0:-0.66
TOTAL 0: 0: 0: 1.33
Total number of warnings issued: 8
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M9 IBD1M9 IBD0M9 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.264 0.491 0.245 3.558 3.632
Variance 0.107 0.070 0.069 1.012 1.164
Minimum 0.001 0.066 0.001 0.000 0.000
Maximum 0.932 0.906 0.934 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.419
2 0.569
3 0.011
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.296
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.23
TOTAL 0: 0: 0: 0.23
Total number of warnings issued: 8
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF10
Note: Opening #include file 1 seldef10
SELECT IBD0M10 IBD1M10 IBD2M10 LDL1 LDL2;
DEFINITION IBD0M10 IBD1M10 IBD2M10;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY10
Note: Opening #include file 1 specify10
SPECIFY K IBD0M10 IBD1M10 IBD2M10
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M10 IBD1M10 IBD0M10 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.265 0.487 0.249 3.558 3.632
Variance 0.112 0.076 0.075 1.012 1.164
Minimum 0.001 0.054 0.001 0.000 0.000
Maximum 0.946 0.907 0.923 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.446
2 0.545
3 0.009
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.281
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.01
Execution 0: 0: 0:-0.59
TOTAL 0: 0: 0: 1.42
Total number of warnings issued: 8
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M10 IBD1M10 IBD0M10 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.265 0.487 0.249 3.558 3.632
Variance 0.112 0.076 0.075 1.012 1.164
Minimum 0.001 0.054 0.001 0.000 0.000
Maximum 0.946 0.907 0.923 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.446
2 0.545
3 0.009
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.281
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.01
Execution 0: 0: 0: 0.12
TOTAL 0: 0: 0: 0.13
Total number of warnings issued: 8
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF11
Note: Opening #include file 1 seldef11
SELECT IBD0M11 IBD1M11 IBD2M11 LDL1 LDL2;
DEFINITION IBD0M11 IBD1M11 IBD2M11;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY11
Note: Opening #include file 1 specify11
SPECIFY K IBD0M11 IBD1M11 IBD2M11
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M11 IBD1M11 IBD0M11 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.266 0.481 0.253 3.558 3.632
Variance 0.124 0.090 0.086 1.012 1.164
Minimum 0.000 0.029 0.000 0.000 0.000
Maximum 0.965 0.941 0.971 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.472
2 0.524
3 0.003
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.265
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.53
Execution 0: 0: 0:-0.98
TOTAL 0: 0: 0: 1.55
Total number of warnings issued: 10
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M11 IBD1M11 IBD0M11 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.266 0.481 0.253 3.558 3.632
Variance 0.124 0.090 0.086 1.012 1.164
Minimum 0.000 0.029 0.000 0.000 0.000
Maximum 0.965 0.941 0.971 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.472
2 0.524
3 0.003
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.265
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.13
TOTAL 0: 0: 0: 0.13
Total number of warnings issued: 10
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF12
Note: Opening #include file 1 seldef12
SELECT IBD0M12 IBD1M12 IBD2M12 LDL1 LDL2;
DEFINITION IBD0M12 IBD1M12 IBD2M12;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY12
Note: Opening #include file 1 specify12
SPECIFY K IBD0M12 IBD1M12 IBD2M12
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M12 IBD1M12 IBD0M12 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.262 0.483 0.255 3.558 3.632
Variance 0.126 0.095 0.091 1.012 1.164
Minimum 0.000 0.006 0.000 0.000 0.000
Maximum 0.973 0.946 0.994 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.485
2 0.511
3 0.004
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.260
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.00
Execution 0: 0: 0:-0.48
TOTAL 0: 0: 0: 1.52
Total number of warnings issued: 10
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M12 IBD1M12 IBD0M12 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.262 0.483 0.255 3.558 3.632
Variance 0.126 0.095 0.091 1.012 1.164
Minimum 0.000 0.006 0.000 0.000 0.000
Maximum 0.973 0.946 0.994 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.485
2 0.511
3 0.004
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.260
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.46
TOTAL 0: 0: 0: 0.46
Total number of warnings issued: 10
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF13
Note: Opening #include file 1 seldef13
SELECT IBD0M13 IBD1M13 IBD2M13 LDL1 LDL2;
DEFINITION IBD0M13 IBD1M13 IBD2M13;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY13
Note: Opening #include file 1 specify13
SPECIFY K IBD0M13 IBD1M13 IBD2M13
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M13 IBD1M13 IBD0M13 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.253 0.493 0.254 3.558 3.632
Variance 0.121 0.097 0.092 1.012 1.164
Minimum 0.000 0.012 0.000 0.000 0.000
Maximum 0.971 0.945 0.988 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.486
2 0.504
3 0.010
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.262
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.99
Execution 0: 0: 0: 0.05
TOTAL 0: 0: 0: 2.04
Total number of warnings issued: 12
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M13 IBD1M13 IBD0M13 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.253 0.493 0.254 3.558 3.632
Variance 0.121 0.097 0.092 1.012 1.164
Minimum 0.000 0.012 0.000 0.000 0.000
Maximum 0.971 0.945 0.988 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.486
2 0.504
3 0.010
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.262
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.838
Saturated model df* >>>>>>>>>>> 413
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 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.14
TOTAL 0: 0: 0: 0.14
Total number of warnings issued: 12
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF14
Note: Opening #include file 1 seldef14
SELECT IBD0M14 IBD1M14 IBD2M14 LDL1 LDL2;
DEFINITION IBD0M14 IBD1M14 IBD2M14;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY14
Note: Opening #include file 1 specify14
SPECIFY K IBD0M14 IBD1M14 IBD2M14
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M14 IBD1M14 IBD0M14 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.243 0.503 0.254 3.558 3.632
Variance 0.125 0.113 0.102 1.012 1.164
Minimum 0.000 0.012 0.000 0.000 0.000
Maximum 0.974 0.955 0.988 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.742
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.015
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.167
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.629
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.028
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.720 0.015 0.027 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.742 0.015 0.028 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.862
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.124
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.742
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.015
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.167
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.629
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.028
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.720 0.015 0.027 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.742 0.015 0.028 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.862
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.124
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.742
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.015
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.487
2 0.499
3 0.014
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.167
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.264
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.028
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.720 0.015 0.027 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.742 0.015 0.028 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.862
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.124
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.832
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.00
Execution 0: 0: 0: 0.27
TOTAL 0: 0: 0: 2.27
Total number of warnings issued: 12
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M14 IBD1M14 IBD0M14 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.243 0.503 0.254 3.558 3.632
Variance 0.125 0.113 0.102 1.012 1.164
Minimum 0.000 0.012 0.000 0.000 0.000
Maximum 0.974 0.955 0.988 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.487
2 0.499
3 0.014
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.264
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.832
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 0.006
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.936
Akaike's Information Criterion > -1.994
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.80
TOTAL 0: 0: 0: 0.80
Total number of warnings issued: 12
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF15
Note: Opening #include file 1 seldef15
SELECT IBD0M15 IBD1M15 IBD2M15 LDL1 LDL2;
DEFINITION IBD0M15 IBD1M15 IBD2M15;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY15
Note: Opening #include file 1 specify15
SPECIFY K IBD0M15 IBD1M15 IBD2M15
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M15 IBD1M15 IBD0M15 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.233 0.514 0.253 3.558 3.632
Variance 0.137 0.144 0.120 1.012 1.164
Minimum 0.000 0.006 0.000 0.000 0.000
Maximum 0.986 0.977 0.994 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.593
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.005
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.432
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.187
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.576 0.005 0.181 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.593 0.005 0.187 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.029
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.770
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.069
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.593
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.005
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.432
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.187
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.576 0.005 0.181 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.593 0.005 0.187 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.029
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.770
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.069
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.593
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.005
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.488
2 0.497
3 0.015
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.432
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.263
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.187
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.576 0.005 0.181 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.593 0.005 0.187 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.029
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.770
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.069
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.491
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 6.76
Execution 0: 0: 0:-4.60
TOTAL 0: 0: 0: 2.16
Total number of warnings issued: 12
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M15 IBD1M15 IBD0M15 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.233 0.514 0.253 3.558 3.632
Variance 0.137 0.144 0.120 1.012 1.164
Minimum 0.000 0.006 0.000 0.000 0.000
Maximum 0.986 0.977 0.994 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.488
2 0.497
3 0.015
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.263
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1099.491
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 0.347
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.556
Akaike's Information Criterion > -1.653
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.90
TOTAL 0: 0: 0: 0.90
Total number of warnings issued: 12
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF16
Note: Opening #include file 1 seldef16
SELECT IBD0M16 IBD1M16 IBD2M16 LDL1 LDL2;
DEFINITION IBD0M16 IBD1M16 IBD2M16;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY16
Note: Opening #include file 1 specify16
SPECIFY K IBD0M16 IBD1M16 IBD2M16
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M16 IBD1M16 IBD0M16 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.226 0.517 0.257 3.558 3.632
Variance 0.138 0.161 0.134 1.012 1.164
Minimum 0.000 0.002 0.000 0.000 0.000
Maximum 0.996 0.998 0.998 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.511
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.002
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.520
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.271
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.497 0.002 0.263 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.511 0.002 0.271 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.029
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.715
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.045
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.511
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.002
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.520
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.271
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.497 0.002 0.263 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.511 0.002 0.271 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.029
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.715
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.045
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.511
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.002
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.491
2 0.497
3 0.013
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.520
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.261
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.271
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.497 0.002 0.263 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.511 0.002 0.271 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.029
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.715
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.045
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1098.959
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.01
Execution 0: 0: 0:-0.60
TOTAL 0: 0: 0: 1.41
Total number of warnings issued: 12
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M16 IBD1M16 IBD0M16 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.226 0.517 0.257 3.558 3.632
Variance 0.138 0.161 0.134 1.012 1.164
Minimum 0.000 0.002 0.000 0.000 0.000
Maximum 0.996 0.998 0.998 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.491
2 0.497
3 0.013
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.261
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1098.959
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 0.879
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.348
Akaike's Information Criterion > -1.121
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.88
TOTAL 0: 0: 0: 0.88
Total number of warnings issued: 12
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF17
Note: Opening #include file 1 seldef17
SELECT IBD0M17 IBD1M17 IBD2M17 LDL1 LDL2;
DEFINITION IBD0M17 IBD1M17 IBD2M17;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY17
Note: Opening #include file 1 specify17
SPECIFY K IBD0M17 IBD1M17 IBD2M17
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M17 IBD1M17 IBD0M17 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.222 0.512 0.266 3.558 3.632
Variance 0.141 0.175 0.149 1.012 1.164
Minimum 0.000 0.001 0.000 0.000 0.000
Maximum 0.998 0.999 0.999 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.453
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.002
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.574
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.329
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.440 0.002 0.320 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.453 0.002 0.329 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.028
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.673
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.040
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.453
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.002
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.574
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.329
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.440 0.002 0.320 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.453 0.002 0.329 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.028
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.673
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.040
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.453
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.002
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.493
2 0.498
3 0.009
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.574
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.258
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.329
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.440 0.002 0.320 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.453 0.002 0.329 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.028
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.673
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.040
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1098.402
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.39
Execution 0: 0: 0:-0.06
TOTAL 0: 0: 0: 2.33
Total number of warnings issued: 14
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M17 IBD1M17 IBD0M17 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.222 0.512 0.266 3.558 3.632
Variance 0.141 0.175 0.149 1.012 1.164
Minimum 0.000 0.001 0.000 0.000 0.000
Maximum 0.998 0.999 0.999 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.493
2 0.498
3 0.009
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.258
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1098.402
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 1.437
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.231
Akaike's Information Criterion > -0.563
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 0.97
TOTAL 0: 0: 0: 0.97
Total number of warnings issued: 14
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF18
Note: Opening #include file 1 seldef18
SELECT IBD0M18 IBD1M18 IBD2M18 LDL1 LDL2;
DEFINITION IBD0M18 IBD1M18 IBD2M18;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY18
Note: Opening #include file 1 specify18
SPECIFY K IBD0M18 IBD1M18 IBD2M18
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M18 IBD1M18 IBD0M18 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.220 0.503 0.276 3.558 3.632
Variance 0.140 0.182 0.162 1.012 1.164
Minimum 0.000 0.000 0.000 0.000 0.000
Maximum 0.998 0.998 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.358
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.650
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.423
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.349 0.000 0.412 0.239
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.358 0.000 0.423 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.027
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.599
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.496
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.358
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.650
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.423
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.349 0.000 0.412 0.239
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.358 0.000 0.423 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.027
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.599
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.496
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.358
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.496
2 0.502
3 0.002
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.650
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.253
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.423
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.349 0.000 0.412 0.239
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.358 0.000 0.423 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.027
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.599
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.496
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1097.273
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.89
Execution 0: 0: 0:-0.49
TOTAL 0: 0: 0: 1.40
Total number of warnings issued: 14
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M18 IBD1M18 IBD0M18 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.220 0.503 0.276 3.558 3.632
Variance 0.140 0.182 0.162 1.012 1.164
Minimum 0.000 0.000 0.000 0.000 0.000
Maximum 0.998 0.998 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.496
2 0.502
3 0.002
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.253
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1097.273
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 2.565
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.109
Akaike's Information Criterion > 0.565
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.14
TOTAL 0: 0: 0: 1.14
Total number of warnings issued: 16
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF19
Note: Opening #include file 1 seldef19
SELECT IBD0M19 IBD1M19 IBD2M19 LDL1 LDL2;
DEFINITION IBD0M19 IBD1M19 IBD2M19;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY19
Note: Opening #include file 1 specify19
SPECIFY K IBD0M19 IBD1M19 IBD2M19
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M19 IBD1M19 IBD0M19 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.215 0.505 0.280 3.558 3.632
Variance 0.125 0.157 0.150 1.012 1.164
Minimum 0.000 0.008 0.000 0.000 0.000
Maximum 0.989 0.980 0.992 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.220
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.748
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.559
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.215 0.000 0.545 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.220 0.000 0.559 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.026
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.469
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.496
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.220
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.748
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.559
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.215 0.000 0.545 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.220 0.000 0.559 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.026
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.469
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.496
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.220
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.593
2 0.406
3 0.002
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.748
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.205
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.559
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.215 0.000 0.545 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.220 0.000 0.559 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.026
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.469
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.496
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1095.521
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.09
Execution 0: 0: 0:-0.37
TOTAL 0: 0: 0: 1.72
Total number of warnings issued: 18
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M19 IBD1M19 IBD0M19 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.215 0.505 0.280 3.558 3.632
Variance 0.125 0.157 0.150 1.012 1.164
Minimum 0.000 0.008 0.000 0.000 0.000
Maximum 0.989 0.980 0.992 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.593
2 0.406
3 0.002
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.205
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1095.521
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 4.317
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.038
Akaike's Information Criterion > 2.317
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.38
TOTAL 0: 0: 0: 1.38
Total number of warnings issued: 18
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF20
Note: Opening #include file 1 seldef20
SELECT IBD0M20 IBD1M20 IBD2M20 LDL1 LDL2;
DEFINITION IBD0M20 IBD1M20 IBD2M20;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY20
Note: Opening #include file 1 specify20
SPECIFY K IBD0M20 IBD1M20 IBD2M20
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M20 IBD1M20 IBD0M20 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.208 0.509 0.282 3.558 3.632
Variance 0.109 0.134 0.137 1.012 1.164
Minimum 0.000 0.013 0.000 0.000 0.000
Maximum 0.984 0.970 0.987 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.101
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.823
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.677
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.099 0.000 0.661 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.101 0.000 0.677 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.024
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.318
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.496
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.101
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.823
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.677
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.099 0.000 0.661 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.101 0.000 0.677 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.024
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.318
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.496
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.101
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.246
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.714
2 0.284
3 0.002
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.823
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.144
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.677
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.099 0.000 0.661 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.101 0.000 0.677 0.246
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.024
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.318
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.496
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1093.428
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.01
Execution 0: 0: 0:-0.13
TOTAL 0: 0: 0: 1.88
Total number of warnings issued: 18
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M20 IBD1M20 IBD0M20 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.208 0.509 0.282 3.558 3.632
Variance 0.109 0.134 0.137 1.012 1.164
Minimum 0.000 0.013 0.000 0.000 0.000
Maximum 0.984 0.970 0.987 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.714
2 0.284
3 0.002
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.144
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1093.428
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 6.410
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.011
Akaike's Information Criterion > 4.410
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.29
TOTAL 0: 0: 0: 1.29
Total number of warnings issued: 18
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF21
Note: Opening #include file 1 seldef21
SELECT IBD0M21 IBD1M21 IBD2M21 LDL1 LDL2;
DEFINITION IBD0M21 IBD1M21 IBD2M21;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY21
Note: Opening #include file 1 specify21
SPECIFY K IBD0M21 IBD1M21 IBD2M21
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M21 IBD1M21 IBD0M21 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.200 0.515 0.284 3.558 3.632
Variance 0.104 0.129 0.133 1.012 1.164
Minimum 0.000 0.011 0.000 0.000 0.000
Maximum 0.985 0.971 0.989 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.033
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.862
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.743
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.032 0.000 0.728 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.033 0.000 0.743 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.021
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.181
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.033
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.862
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.743
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.032 0.000 0.728 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.033 0.000 0.743 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.021
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.181
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.033
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.840
2 0.160
3 0.001
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.862
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.081
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.743
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.032 0.000 0.728 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.033 0.000 0.743 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.021
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.181
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1091.458
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.97
Execution 0: 0: 0: 0.08
TOTAL 0: 0: 0: 2.05
Total number of warnings issued: 18
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M21 IBD1M21 IBD0M21 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.200 0.515 0.284 3.558 3.632
Variance 0.104 0.129 0.133 1.012 1.164
Minimum 0.000 0.011 0.000 0.000 0.000
Maximum 0.985 0.971 0.989 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.840
2 0.160
3 0.001
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.081
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1091.458
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 8.380
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.004
Akaike's Information Criterion > 6.380
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.10
TOTAL 0: 0: 0: 1.10
Total number of warnings issued: 18
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF22
Note: Opening #include file 1 seldef22
SELECT IBD0M22 IBD1M22 IBD2M22 LDL1 LDL2;
DEFINITION IBD0M22 IBD1M22 IBD2M22;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY22
Note: Opening #include file 1 specify22
SPECIFY K IBD0M22 IBD1M22 IBD2M22
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M22 IBD1M22 IBD0M22 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.192 0.523 0.286 3.558 3.632
Variance 0.110 0.142 0.137 1.012 1.164
Minimum 0.000 0.003 0.000 0.000 0.000
Maximum 0.992 0.985 0.997 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.010
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.244
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.875
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.765
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.010 0.750 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.010 0.765 0.244
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.020
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.101
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.494
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.010
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.244
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.875
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.765
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.010 0.750 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.010 0.765 0.244
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.020
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.101
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.494
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.010
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.244
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.970
2 0.030
3 0.000
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.875
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.631
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.015
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.765
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.010 0.750 0.240
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.010 0.765 0.244
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.020
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.101
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.494
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1089.801
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.03
Execution 0: 0: 0: 0.36
TOTAL 0: 0: 0: 2.39
Total number of warnings issued: 20
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M22 IBD1M22 IBD0M22 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.192 0.523 0.286 3.558 3.632
Variance 0.110 0.142 0.137 1.012 1.164
Minimum 0.000 0.003 0.000 0.000 0.000
Maximum 0.992 0.985 0.997 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.970
2 0.030
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.015
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1089.801
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 10.037
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.002
Akaike's Information Criterion > 8.037
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.43
TOTAL 0: 0: 0: 1.43
Total number of warnings issued: 20
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF23
Note: Opening #include file 1 seldef23
SELECT IBD0M23 IBD1M23 IBD2M23 LDL1 LDL2;
DEFINITION IBD0M23 IBD1M23 IBD2M23;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY23
Note: Opening #include file 1 specify23
SPECIFY K IBD0M23 IBD1M23 IBD2M23
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M23 IBD1M23 IBD0M23 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.187 0.524 0.290 3.558 3.632
Variance 0.096 0.128 0.133 1.012 1.164
Minimum 0.000 0.009 0.000 0.000 0.000
Maximum 0.985 0.973 0.991 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.240
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.881
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.776
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.764 0.236
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.776 0.240
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.016
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.490
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.240
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.881
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.776
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.764 0.236
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.776 0.240
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.016
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.490
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.240
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.909
2 0.090
3 0.000
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.881
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.632
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.045
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.776
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.764 0.236
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.776 0.240
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.016
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.490
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1088.010
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.83
Execution 0: 0: 0: 0.57
TOTAL 0: 0: 0: 2.40
Total number of warnings issued: 22
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M23 IBD1M23 IBD0M23 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.187 0.524 0.290 3.558 3.632
Variance 0.096 0.128 0.133 1.012 1.164
Minimum 0.000 0.009 0.000 0.000 0.000
Maximum 0.985 0.973 0.991 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.909
2 0.090
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.045
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1088.010
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 11.828
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.001
Akaike's Information Criterion > 9.828
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.30
TOTAL 0: 0: 0: 1.30
Total number of warnings issued: 22
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF24
Note: Opening #include file 1 seldef24
SELECT IBD0M24 IBD1M24 IBD2M24 LDL1 LDL2;
DEFINITION IBD0M24 IBD1M24 IBD2M24;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY24
Note: Opening #include file 1 specify24
SPECIFY K IBD0M24 IBD1M24 IBD2M24
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M24 IBD1M24 IBD0M24 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.182 0.525 0.294 3.558 3.632
Variance 0.086 0.118 0.132 1.012 1.164
Minimum 0.000 0.014 0.000 0.000 0.000
Maximum 0.979 0.963 0.986 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.237
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.633
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.775
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.766 0.234
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.775 0.237
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.012
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.487
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.237
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.633
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.775
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.766 0.234
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.775 0.237
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.012
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.487
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.237
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.799
2 0.200
3 0.001
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.633
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.101
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.775
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.766 0.234
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.775 0.237
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.012
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.487
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1086.479
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.82
Execution 0: 0: 0: 0.10
TOTAL 0: 0: 0: 1.92
Total number of warnings issued: 22
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M24 IBD1M24 IBD0M24 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.182 0.525 0.294 3.558 3.632
Variance 0.086 0.118 0.132 1.012 1.164
Minimum 0.000 0.014 0.000 0.000 0.000
Maximum 0.979 0.963 0.986 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.799
2 0.200
3 0.001
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.101
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1086.479
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 13.359
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 11.359
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.25
TOTAL 0: 0: 0: 1.25
Total number of warnings issued: 22
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF25
Note: Opening #include file 1 seldef25
SELECT IBD0M25 IBD1M25 IBD2M25 LDL1 LDL2;
DEFINITION IBD0M25 IBD1M25 IBD2M25;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY25
Note: Opening #include file 1 specify25
SPECIFY K IBD0M25 IBD1M25 IBD2M25
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M25 IBD1M25 IBD0M25 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.176 0.527 0.298 3.558 3.632
Variance 0.086 0.123 0.135 1.012 1.164
Minimum 0.000 0.013 0.000 0.000 0.000
Maximum 0.982 0.965 0.987 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.235
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.633
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.773
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.767 0.233
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.773 0.235
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.009
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.485
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.235
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.633
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.773
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.767 0.233
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.773 0.235
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.009
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.485
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.235
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.693
2 0.305
3 0.002
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.633
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.154
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.773
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.767 0.233
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.773 0.235
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.009
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.485
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1085.112
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.90
Execution 0: 0: 0: 0.17
TOTAL 0: 0: 0: 2.07
Total number of warnings issued: 22
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M25 IBD1M25 IBD0M25 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.176 0.527 0.298 3.558 3.632
Variance 0.086 0.123 0.135 1.012 1.164
Minimum 0.000 0.013 0.000 0.000 0.000
Maximum 0.982 0.965 0.987 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.693
2 0.305
3 0.002
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.154
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1085.112
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 14.726
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 12.726
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.47
TOTAL 0: 0: 0: 1.47
Total number of warnings issued: 22
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF26
Note: Opening #include file 1 seldef26
SELECT IBD0M26 IBD1M26 IBD2M26 LDL1 LDL2;
DEFINITION IBD0M26 IBD1M26 IBD2M26;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY26
Note: Opening #include file 1 specify26
SPECIFY K IBD0M26 IBD1M26 IBD2M26
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M26 IBD1M26 IBD0M26 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.168 0.530 0.301 3.558 3.632
Variance 0.097 0.144 0.145 1.012 1.164
Minimum 0.000 0.006 0.000 0.000 0.000
Maximum 0.991 0.979 0.994 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.234
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.773
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.768 0.232
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.773 0.234
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.484
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.234
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.773
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.768 0.232
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.773 0.234
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.484
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.234
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.590
2 0.409
3 0.001
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.205
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.773
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.768 0.232
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.773 0.234
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.484
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1083.763
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.09
Execution 0: 0: 0:-0.27
TOTAL 0: 0: 0: 1.82
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M26 IBD1M26 IBD0M26 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.168 0.530 0.301 3.558 3.632
Variance 0.097 0.144 0.145 1.012 1.164
Minimum 0.000 0.006 0.000 0.000 0.000
Maximum 0.991 0.979 0.994 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.590
2 0.409
3 0.001
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.205
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1083.763
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 16.075
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 14.075
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.19
TOTAL 0: 0: 0: 1.19
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF27
Note: Opening #include file 1 seldef27
SELECT IBD0M27 IBD1M27 IBD2M27 LDL1 LDL2;
DEFINITION IBD0M27 IBD1M27 IBD2M27;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY27
Note: Opening #include file 1 specify27
SPECIFY K IBD0M27 IBD1M27 IBD2M27
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M27 IBD1M27 IBD0M27 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.157 0.539 0.304 3.558 3.632
Variance 0.108 0.165 0.150 1.012 1.164
Minimum 0.000 0.000 0.000 0.000 0.000
Maximum 0.997 0.997 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.234
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.768 0.232
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.234
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.008
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.484
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.234
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.768 0.232
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.234
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.008
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.484
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.234
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.555
2 0.445
3 0.000
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.223
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.768 0.232
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.234
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.008
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.484
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1084.097
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.90
Execution 0: 0: 0:-0.13
TOTAL 0: 0: 0: 1.77
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M27 IBD1M27 IBD0M27 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.157 0.539 0.304 3.558 3.632
Variance 0.108 0.165 0.150 1.012 1.164
Minimum 0.000 0.000 0.000 0.000 0.000
Maximum 0.997 0.997 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.555
2 0.445
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.223
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1084.097
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 15.741
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 13.741
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.29
TOTAL 0: 0: 0: 1.29
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF28
Note: Opening #include file 1 seldef28
SELECT IBD0M28 IBD1M28 IBD2M28 LDL1 LDL2;
DEFINITION IBD0M28 IBD1M28 IBD2M28;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY28
Note: Opening #include file 1 specify28
SPECIFY K IBD0M28 IBD1M28 IBD2M28
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M28 IBD1M28 IBD0M28 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.161 0.538 0.301 3.558 3.632
Variance 0.090 0.129 0.130 1.012 1.164
Minimum 0.000 0.014 0.000 0.000 0.000
Maximum 0.980 0.967 0.986 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.235
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.772
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.767 0.233
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.772 0.235
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.485
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.235
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.772
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.767 0.233
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.772 0.235
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.485
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.235
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.600
2 0.397
3 0.004
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.202
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.772
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.767 0.233
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.772 0.235
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.485
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1085.124
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.85
Execution 0: 0: 0:-0.10
TOTAL 0: 0: 0: 1.75
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M28 IBD1M28 IBD0M28 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.161 0.538 0.301 3.558 3.632
Variance 0.090 0.129 0.130 1.012 1.164
Minimum 0.000 0.014 0.000 0.000 0.000
Maximum 0.980 0.967 0.986 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.600
2 0.397
3 0.004
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.202
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1085.124
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 14.714
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 12.714
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.43
TOTAL 0: 0: 0: 1.43
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF29
Note: Opening #include file 1 seldef29
SELECT IBD0M29 IBD1M29 IBD2M29 LDL1 LDL2;
DEFINITION IBD0M29 IBD1M29 IBD2M29;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY29
Note: Opening #include file 1 specify29
SPECIFY K IBD0M29 IBD1M29 IBD2M29
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M29 IBD1M29 IBD0M29 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.165 0.537 0.298 3.558 3.632
Variance 0.080 0.110 0.120 1.012 1.164
Minimum 0.000 0.022 0.000 0.000 0.000
Maximum 0.969 0.952 0.978 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.236
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.771
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.766 0.234
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.771 0.236
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.486
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.236
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.771
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.766 0.234
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.771 0.236
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.486
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.236
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.647
2 0.348
3 0.005
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.179
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.771
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.766 0.234
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.771 0.236
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.007
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.486
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1085.991
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.82
Execution 0: 0: 0: 0.06
TOTAL 0: 0: 0: 1.88
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M29 IBD1M29 IBD0M29 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.165 0.537 0.298 3.558 3.632
Variance 0.080 0.110 0.120 1.012 1.164
Minimum 0.000 0.022 0.000 0.000 0.000
Maximum 0.969 0.952 0.978 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.647
2 0.348
3 0.005
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.179
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1085.991
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 13.847
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 11.847
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.26
TOTAL 0: 0: 0: 1.26
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF30
Note: Opening #include file 1 seldef30
SELECT IBD0M30 IBD1M30 IBD2M30 LDL1 LDL2;
DEFINITION IBD0M30 IBD1M30 IBD2M30;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY30
Note: Opening #include file 1 specify30
SPECIFY K IBD0M30 IBD1M30 IBD2M30
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M30 IBD1M30 IBD0M30 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.168 0.536 0.296 3.558 3.632
Variance 0.077 0.105 0.117 1.012 1.164
Minimum 0.000 0.024 0.000 0.000 0.000
Maximum 0.965 0.948 0.976 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.237
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.635
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.771
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.765 0.235
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.771 0.237
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.008
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.487
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.237
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.635
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.771
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.765 0.235
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.771 0.237
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.008
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.487
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.237
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.696
2 0.299
3 0.005
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.635
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.155
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.771
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.765 0.235
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.771 0.237
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.008
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.487
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1086.771
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.07
Execution 0: 0: 0:-0.13
TOTAL 0: 0: 0: 1.94
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M30 IBD1M30 IBD0M30 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.168 0.536 0.296 3.558 3.632
Variance 0.077 0.105 0.117 1.012 1.164
Minimum 0.000 0.024 0.000 0.000 0.000
Maximum 0.965 0.948 0.976 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.696
2 0.299
3 0.005
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.155
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1086.771
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 13.068
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 11.068
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.32
TOTAL 0: 0: 0: 1.32
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF31
Note: Opening #include file 1 seldef31
SELECT IBD0M31 IBD1M31 IBD2M31 LDL1 LDL2;
DEFINITION IBD0M31 IBD1M31 IBD2M31;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY31
Note: Opening #include file 1 specify31
SPECIFY K IBD0M31 IBD1M31 IBD2M31
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M31 IBD1M31 IBD0M31 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.170 0.536 0.294 3.558 3.632
Variance 0.082 0.113 0.122 1.012 1.164
Minimum 0.000 0.020 0.000 0.000 0.000
Maximum 0.968 0.955 0.980 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.238
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.635
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.772
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.764 0.236
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.772 0.238
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.010
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.488
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.238
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.635
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.772
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.764 0.236
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.772 0.238
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.010
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.488
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.238
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.748
2 0.248
3 0.004
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.879
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.635
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.128
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.772
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.764 0.236
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.772 0.238
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.010
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.488
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1087.503
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.01
Execution 0: 0: 0:-0.13
TOTAL 0: 0: 0: 1.88
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M31 IBD1M31 IBD0M31 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.170 0.536 0.294 3.558 3.632
Variance 0.082 0.113 0.122 1.012 1.164
Minimum 0.000 0.020 0.000 0.000 0.000
Maximum 0.968 0.955 0.980 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.748
2 0.248
3 0.004
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.128
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1087.503
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 12.335
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.000
Akaike's Information Criterion > 10.335
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.01
Execution 0: 0: 0: 1.20
TOTAL 0: 0: 0: 1.21
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF32
Note: Opening #include file 1 seldef32
SELECT IBD0M32 IBD1M32 IBD2M32 LDL1 LDL2;
DEFINITION IBD0M32 IBD1M32 IBD2M32;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY32
Note: Opening #include file 1 specify32
SPECIFY K IBD0M32 IBD1M32 IBD2M32
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M32 IBD1M32 IBD0M32 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.172 0.535 0.292 3.558 3.632
Variance 0.095 0.135 0.134 1.012 1.164
Minimum 0.000 0.010 0.000 0.000 0.000
Maximum 0.978 0.974 0.990 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.240
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.636
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.763 0.237
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.240
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.014
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.490
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.240
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.636
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.763 0.237
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.240
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.014
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.490
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.240
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.804
2 0.194
3 0.002
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.636
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.099
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.763 0.237
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.240
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.014
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.490
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1088.237
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.82
Execution 0: 0: 0:-0.08
TOTAL 0: 0: 0: 1.74
Total number of warnings issued: 24
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M32 IBD1M32 IBD0M32 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.172 0.535 0.292 3.558 3.632
Variance 0.095 0.135 0.134 1.012 1.164
Minimum 0.000 0.010 0.000 0.000 0.000
Maximum 0.978 0.974 0.990 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.804
2 0.194
3 0.002
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.099
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1088.237
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 11.601
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.001
Akaike's Information Criterion > 9.601
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.28
TOTAL 0: 0: 0: 1.28
Total number of warnings issued: 24
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF33
Note: Opening #include file 1 seldef33
SELECT IBD0M33 IBD1M33 IBD2M33 LDL1 LDL2;
DEFINITION IBD0M33 IBD1M33 IBD2M33;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY33
Note: Opening #include file 1 specify33
SPECIFY K IBD0M33 IBD1M33 IBD2M33
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M33 IBD1M33 IBD0M33 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.178 0.531 0.290 3.558 3.632
Variance 0.108 0.156 0.148 1.012 1.164
Minimum 0.000 0.001 0.000 0.000 0.000
Maximum 0.990 0.992 0.999 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.242
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.636
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.762 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.242
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.016
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.492
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.242
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.636
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.762 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.242
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.016
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.492
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.242
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.871
2 0.129
3 0.000
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.880
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.636
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.065
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.774
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.762 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.774 0.242
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.016
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.492
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1088.731
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.82
Execution 0: 0: 0: 0.13
TOTAL 0: 0: 0: 1.95
Total number of warnings issued: 26
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M33 IBD1M33 IBD0M33 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.178 0.531 0.290 3.558 3.632
Variance 0.108 0.156 0.148 1.012 1.164
Minimum 0.000 0.001 0.000 0.000 0.000
Maximum 0.990 0.992 0.999 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.871
2 0.129
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.065
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1088.731
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 11.107
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.001
Akaike's Information Criterion > 9.107
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.29
TOTAL 0: 0: 0: 1.29
Total number of warnings issued: 26
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF34
Note: Opening #include file 1 seldef34
SELECT IBD0M34 IBD1M34 IBD2M34 LDL1 LDL2;
DEFINITION IBD0M34 IBD1M34 IBD2M34;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY34
Note: Opening #include file 1 specify34
SPECIFY K IBD0M34 IBD1M34 IBD2M34
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M34 IBD1M34 IBD0M34 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.191 0.521 0.288 3.558 3.632
Variance 0.122 0.171 0.156 1.012 1.164
Minimum 0.000 0.001 0.000 0.000 0.000
Maximum 0.997 0.997 0.999 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.247
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.637
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.770
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.757 0.243
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.770 0.247
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.018
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.497
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.247
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.637
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.770
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.757 0.243
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.770 0.247
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.018
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.497
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.000
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.247
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.953
2 0.047
3 0.000
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.878
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.637
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.024
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.770
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.000 0.000 0.757 0.243
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.000 0.000 0.770 0.247
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.018
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.497
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1089.523
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 2.22
Execution 0: 0: 0:-0.68
TOTAL 0: 0: 0: 1.54
Total number of warnings issued: 28
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M34 IBD1M34 IBD0M34 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.191 0.521 0.288 3.558 3.632
Variance 0.122 0.171 0.156 1.012 1.164
Minimum 0.000 0.001 0.000 0.000 0.000
Maximum 0.997 0.997 0.999 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.953
2 0.047
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.024
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1089.523
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 10.315
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.001
Akaike's Information Criterion > 8.315
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.23
TOTAL 0: 0: 0: 1.23
Total number of warnings issued: 28
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF35
Note: Opening #include file 1 seldef35
SELECT IBD0M35 IBD1M35 IBD2M35 LDL1 LDL2;
DEFINITION IBD0M35 IBD1M35 IBD2M35;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY35
Note: Opening #include file 1 specify35
SPECIFY K IBD0M35 IBD1M35 IBD2M35
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _
H@A+C+P@Q | A+C+Q+E;
START 1 ALL
START 2.8 M 1 1 1
OPTION NDECIMALS=3
OPTION MULTIPLE ISSAT
END
Summary of VL file data for group 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M35 IBD1M35 IBD0M35 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.217 0.498 0.286 3.558 3.632
Variance 0.136 0.176 0.161 1.012 1.164
Minimum 0.000 0.000 0.000 0.000 0.000
Maximum 1.000 1.000 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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
*** 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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.144
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.250
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.792
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.627
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.141 0.000 0.614 0.245
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.144 0.000 0.627 0.250
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.021
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.379
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.500
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.144
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.250
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.792
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.627
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.141 0.000 0.614 0.245
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.144 0.000 0.627 0.250
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.021
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.379
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.500
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.144
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.000
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.250
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.996
2 0.004
3 0.000
MATRIX L
This is a FULL matrix of order 1 by 1
1
1 0.792
MATRIX M
This is a FULL matrix of order 1 by 1
1
1 3.634
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.002
MATRIX Q
This is a computed FULL matrix of order 1 by 1
[=L*L']
1
1 0.627
MATRIX S
This is a computed FULL matrix of order 1 by 4
[=T@V~]
A^2 C^2 Q^2 E^2
STANDEST 0.141 0.000 0.614 0.245
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.144 0.000 0.627 0.250
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.021
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.379
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.000
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.500
*** WARNING! ***
Minimization may not be successful. See above
CODE GREEN - it probably was OK
Your model has 5 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1093.579
Degrees of freedom >>>>>>>>>>>>>>>> 413
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 1.82
Execution 0: 0: 0:-0.36
TOTAL 0: 0: 0: 1.46
Total number of warnings issued: 30
______________________________________________________________________________
! 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 2
LDL1 LDL2
Code 1.000 2.000
Number 92.000 92.000
Mean 3.648 3.719
Variance 1.100 0.749
Minimum 0.000 1.730
Maximum 5.980 5.960
Summary of VL file data for group 3
IBD2M35 IBD1M35 IBD0M35 LDL1 LDL2
Code -3.000 -2.000 -1.000 1.000 2.000
Number 117.000 117.000 117.000 117.000 117.000
Mean 0.217 0.498 0.286 3.558 3.632
Variance 0.136 0.176 0.161 1.012 1.164
Minimum 0.000 0.000 0.000 0.000 0.000
Maximum 1.000 1.000 1.000 5.650 6.390
PARAMETER SPECIFICATIONS
GROUP NUMBER: 1
G1: Parameter Estimates
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 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 U
This is a UNIT matrix of order 1 by 2
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: 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 H
This is a 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 U
This is a UNIT matrix of order 1 by 2
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: 3
G3: 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 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 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 U
This is a UNIT matrix of order 1 by 2
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: Parameter Estimates
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 2
G2: MZ twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
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 3.629
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
GROUP NUMBER: 3
G3: Dizygotic twins
MATRIX A
This is a computed FULL matrix of order 1 by 1
[=X*X']
1
1 0.769
MATRIX C
This is a computed FULL matrix of order 1 by 1
[=Y*Y']
1
1 0.018
MATRIX E
This is a computed FULL matrix of order 1 by 1
[=Z*Z']
1
1 0.245
MATRIX H
This is a FULL matrix of order 1 by 1
1
1 0.500
MATRIX J
This is a FULL matrix of order 1 by 3
1 2 3
1 0.000 0.500 1.000
MATRIX K
This is a FULL matrix of order 3 by 1
1
1 0.996
2 0.004
3 0.000
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 3.629
MATRIX P
This is a computed FULL matrix of order 1 by 1
[=J*K]
1
1 0.002
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 C^2 Q^2 E^2
STANDEST 0.745 0.017 0.000 0.238
MATRIX T
This is a computed FULL matrix of order 1 by 4
[=A|C|Q|E]
A^2 C^2 Q^2 E^2
UNSTANDEST 0.769 0.018 0.000 0.245
MATRIX U
This is a UNIT matrix of order 1 by 2
MATRIX V
This is a computed FULL matrix of order 1 by 1
[=A+C+Q+E]
1
1 1.031
MATRIX X
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.877
MATRIX Y
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 0.133
MATRIX Z
This is a LOWER TRIANGULAR matrix of order 1 by 1
1
1 -0.495
Your model has 4 estimated parameters and 418 Observed statistics
-2 times log-likelihood of data >>> 1099.838
Degrees of freedom >>>>>>>>>>>>>>>> 414
Saturated model fit* >>>>>>>>>>> 1093.579
Saturated model df* >>>>>>>>>>> 413
Difference Chi-squared >>>>>>>> 6.259
Difference d.f. >>>>>>>>>>>>>>> 1
Probability >>>>>>>>>>>>>>>>>>>> 0.012
Akaike's Information Criterion > 4.259
* Saturated model statistic computed earlier in this job
This problem used 1.6% of my workspace
Task Time elapsed (DD:HH:MM:SS)
Reading script & data 0: 0: 0: 0.00
Execution 0: 0: 0: 1.68
TOTAL 0: 0: 0: 1.68
Total number of warnings issued: 30
______________________________________________________________________________
The following MX script lines were read for group 1
#DEFINE NVAR 1
Note: Global variable previously defined. Updated: NVAR
#DEFINE NSIB 2 !NUMBER OF SIBLINGS
Note: Global variable previously defined. Updated: NSIB
#NGROUPS 3
Note: #NGroup set number of groups to 3
G1: PARAMETER ESTIMATES
CALCULATION
BEGIN MATRICES;
X LOWER NVAR NVAR FREE !ADDITIVE GENETIC PARAMETER
Y LOWER NVAR NVAR FREE !SHARED ENVIRONMENTAL PARAMETER
Z LOWER NVAR NVAR FREE !UNIQUE ENVIRONMENTAL PARAMETER
L FULL NVAR 1 FREE !QTL EFFECT
M FULL 1 NVAR FREE !MEANS
U UNIT 1 NSIB
H FULL 1 1
END MATRICES;
MATRIX H .5
BEGIN ALGEBRA;
A= X*X'; !ADDITIVE GENETIC VARIANCE
C= Y*Y'; !SHARED ENVIRONMENTAL VARIANCE
E= Z*Z'; !UNIQUE ENVIRONMENTAL VARIANCE
Q= L*L'; !VARIANCE DUE TO QTL
V= A+C+Q+E; !TOTAL VARIANCE
T= A|C|Q|E; !PARAMETERS IN ONE MATRIX FOR STANDARDIZING
S= T@V~; !STANDARDIZED VARIANCE COMPONENT ESTIMATES
END ALGEBRA;
LABELS ROW S STANDEST
LABELS COL S A^2 C^2 Q^2 E^2
LABELS ROW T UNSTANDEST
LABELS COL T A^2 C^2 Q^2 E^2
END
The following MX script lines were read for group 2
G2: MZ TWINS
#INCLUDE LIPIDMZ.DAT
Note: Opening #include file 1 lipidmz.dat
DATA NINPUTVARS=14 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDMZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 92 records with data
that contained a total of 1288 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 SEX1 AGE1 LDL1 APOB1 LNAPOE1
NIH_ID2 SEX2 AGE2 LDL2 APOB2 LNAPOE2
Note: Closing #include file 1
SELECT LDL1 LDL2;
BEGIN MATRICES = GROUP 1;
NOTE: Selection yields 92 data vectors for analysis
NOTE: Vectors contain a total of 184 observations
MEANS U@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 3
G3: DIZYGOTIC TWINS
#INCLUDE LIPIDDZ.DAT
Note: Opening #include file 1 lipiddz.dat
DATA NINPUTVARS=182 NOBSERVATIONS=0
RECTANGULAR FILE=LIPIDDZ.REC
Rectangular continuous data read initiated
NOTE: Rectangular file contained 117 records with data
that contained a total of 21286 observations
MISSING=-1.00
NOTE: Missing value *string* set to '-1.00'
LABELS
FAM ZYG1_5
NIH_ID1 LIPIDME1 SEX1 AGE1 LDL1 APOB1 APOE1 LNAPOE1
NIH_ID2 LIPIDME2 SEX2 AGE2 LDL2 APOB2 APOE2 LNAPOE2
PIHAT65 PI65CAT
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
Note: Closing #include file 1
#INCLUDE SELDEF36
Note: Opening #include file 1 seldef36
SELECT IBD0M36 IBD1M36 IBD2M36 LDL1 LDL2;
DEFINITION IBD0M36 IBD1M36 IBD2M36;
NOTE: Selection yields 117 data vectors for analysis
NOTE: Vectors contain a total of 585 observations
Note: Closing #include file 1
BEGIN MATRICES = GROUP 1;
NOTE: Definition yields 117 data vectors for analysis
NOTE: Vectors contain a total of 234 observations
K FULL 3 1 !IBD PROBABILITIES (FROM MERLIN)
J FULL 1 3 !COEFFICIENTS 0,0.5,1 FOR PIHAT
END MATRICES;
#INCLUDE SPECIFY36
Note: Opening #include file 1 specify36
SPECIFY K IBD0M36 IBD1M36 IBD2M36
Note: Closing #include file 1
MATRIX J 0. 0.5 1.0
BEGIN ALGEBRA;
P= J*K; !ESTIMATE OF PIHAT
END ALGEBRA;
MEANS U@M;
COVARIANCE A+C+Q+E | H@A+C+P@Q _