Bivariate anaysis + maternal genetic effect for both traits
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Bivariate anaysis + maternal genetic effect for both traits
Dear asreml users
Hi and merry cristmass and happy ney year
I would like to set up an ASREML to do a bivariate analysis for traits with
maternal genetic effect for both.
I set up the following . as file . But I am not sure for results, because in
Asr file there are 13 variance componenet with a warning! (Code B) and this is
not correct ,because it should be 12 component and no 13 .
Would you please check my .as File and tell me my mistakes
Any help greatly appreciated.
Best regards
abbas
The .as file
Bivariate Analysis for BW & TV
IND !P
SIRE
DAM !P
IHD 46 !I
SEX 2 !I
K 2 !I
AFDEL 10 !I
HCT !M -99
GEW !M -99
RV !M -99
TV !M -99
RATIO !M -99
PERRV !M -99
PERTV !M -99
UITV !M -99
VOCHT !M -99
BORST !M -99
LEVER !M -99
HART !M -99 # DEPENDENT VARIABLES
ali2.prn !MAKE #pedigree file
ali1.prn !MAXIT 50 #ascites data
GEW TV ~ Trait Tr.SEX Tr.K Tr.AFDEL Tr.IHD !r Tr.IND Tr.DAM !f mv
1 2 1
0 0 0
2 0 US 4.14 -2.58 8.22 !GP # residual variance
Tr.IND 2
4 0 US 1.23 0.31 0.22 !GP
5327 0 0
ASR FILE :
ASREML [11 Jun 1999] Bivariate Analysis for BW & TV
Tue Dec 25 10:49:29 2001 64.00 Mbyte mgew3
Reading ali2.prn : skipping 0 lines
PEDIGREE [ali2.prn ] has 5327 identities, 16760 Non zero elements
QUALIFIERS: !MAXIT 50
Reading ali1.prn FREE FORMAT skipping 0 lines
Bivariate analysis of GEW and TV
Using 4202 records [of 4202 read from 4202 lines of ali1.prn
]
Model term Size Type COL Minimum Mean Maximum #zero
#miss
1 IND 5327 Direct 1 895.0 3102. 5327. 0
0
2 SIRE 1 Covariat 2 0.9413E+08 0.9420E+08 0.9429E+08 0
0
3 DAM 5327 Direct 3 66.00 453.2 892.0 0
0
4 IHD 46 Factor 4 1 22.6675 46 0
0
5 SEX 2 Factor 5 1 1.5869 2 0
0
6 K 2 Factor 6 1 1.8377 2 0
0
7 AFDEL 10 Factor 7 1 4.9912 10 0
0
8 HCT 1 Covariat 8 23.00 35.40 55.00 0
655
9 GEW 1 Variate 9 3.540 16.04 25.63 0
509
10 RV 1 Covariat 10 0.4000 1.955 5.300 0
542
11 TV 1 Variate 11 2.300 6.968 11.80 0
544
12 RATIO 1 Covariat 12 8.000 27.94 60.00 0
544
13 PERRV 1 Covariat 13 2.747 12.47 51.50 0
556
14 PERTV 1 Covariat 14 2.238 4.393 9.002 0
558
15 UITV 1 Covariat 15 1.000 0.1600 1.000 2095
1708
16 VOCHT 1 Covariat 16 1.000 0.7763E-01 2.000 3542
505
17 BORST 1 Covariat 17 1.000 0.3084E-01 2.000 3585
505
18 LEVER 1 Covariat 18 1.000 0.6708E-01 2.000 3488
505
19 HART 1 Covariat 19 1.000 0.5890 2.000 1781
506
20 Trait 2 Traits/Variat
21 Tr.SEX 4 Interaction 20 Trait : 2 5 SEX :
2
22 Tr.K 4 Interaction 20 Trait : 2 6 K :
2
23 Tr.AFDEL 20 Interaction 20 Trait : 2 7 AFDEL :
10
24 Tr.IHD 92 Interaction 20 Trait : 2 4 IHD :
46
25 Tr.IND 10654 Interaction 20 Trait : 2 1 IND :
5327
26 Tr.DAM 10654 Interaction 20 Trait : 2 3 DAM :
5327
27 mv_estimates 1053 Missing value
4202 identity
2 US=UnStr 4.14 -2.58 8.22
8404 records assumed sorted 2 within 4202
Eigen analysis check of US matrix failed
4 US=UnStr 1.23 0.31 0.22 0.00 0.00 1.30 0.00
0.00
0.00 1.40
5327 Ainverse
Structure of Tr.IND has 21308 levels defined
Forming 22484 equations: 123 dense
Initial updates will be shrunk by factor 0.245
NOTICE: 1073 (more) singularities,
LogL=-9520.72 S2= 1.0000 8302 df 1.0000 4.1400 -2.5800
8.2200 1.2300 0.31000 0.22000 0.0000 0.0000 1.3000
0.0000 0.0000 0.0000 1.4000
LogL=-8614.48 S2= 1.0000 8302 df2 1.0000 0.60852 0.61483
0.62747 1.4452 0.29231E-01 1.5344 -.79220E-010.79747E-010.98975
0.36558 -.12591 0.25843 0.19325
LogL=-7855.51 S2= 1.0000 8302 df1 1.0000 0.95791 0.11343
1.2687 1.3974 0.20898 0.28709 0.54146 0.38340E-020.23705
0.44319 0.83408E-010.17526 0.32174
LogL=-7855.51 S2= 1.0000 8302 df 1.0000 0.95791 0.11343
1.2687 1.3974 0.20898 0.28709 0.54146 0.38340E-020.23705
0.44319 0.83408E-010.17526 0.32174
Final parameter values 1.0000 0.95791 0.11343
1.2687 1.3974 0.20898 0.28709 0.54146 0.38340E-020.23705
0.44319 0.83408E-010.17526 0.32174
Source Model terms Gamma Component Comp/SE % C
Residual US=UnStr 1 0.957908 0.957908 0.00 0 B
Residual US=UnStr 1 0.113433 0.113433 0.00 0 B
Residual US=UnStr 2 1.26866 1.26866 0.00 0
B
Tr.IND US=UnStr 1 1.39739 1.39739 0.00 0
B
Tr.IND US=UnStr 1 0.208978 0.208978 0.00 0 B
Tr.IND US=UnStr 2 0.287092 0.287092 0.00 0 B
Tr.IND US=UnStr 1 0.541459 0.541459 0.00 0 B
Tr.IND US=UnStr 2 0.383401E-02 0.383401E-02 0.00 0 B
Tr.IND US=UnStr 3 0.237048 0.237048 0.00 0 B
Tr.IND US=UnStr 1 0.443194 0.443194 0.00 0 B
Tr.IND US=UnStr 2 0.834078E-01 0.834078E-01 0.00 0 B
Tr.IND US=UnStr 3 0.175257 0.175257 0.00 0 B
Tr.IND US=UnStr 4 0.321736 0.321736 0.00 0 B
WARNING: Code B - fixed at a boundary (!GP)
C - Constrained by user (!CON)
S - Singular Information matrix
S means there is no information in the data for this parameter.
Very small components with Comp/SE ratios of zero sometimes indicate poor
scaling. Consider rescaling the design matrix in such cases
Covariance/Variance/Correlation Matrix US=UnStructu
0.9579 0.1029
0.1134 1.269
Covariance/Variance/Correlation Matrix US=UnStructu
1.397 0.3299 0.9408 0.6610
0.2090 0.2871 0.1470E-01 0.2744
0.5415 0.3834E-02 0.2370 0.6346
0.4432 0.8341E-01 0.1753 0.3217
Analysis of Variance DF F-incr F-adj StndErrDiff
20 Trait 2 767.53 462.44
21 Tr.SEX 2 1001.86 1014.43
22 Tr.K 2 50.34 39.38
23 Tr.AFDEL 16 65.54 32.31
24 Tr.IHD 80 2.08 2.08
Solution Standard Error T-value T-prev
24 Tr.IHD
2 0.706798 0.342184 2.07
3 0.685431 0.355392 1.93 -0.08
5 0.330419 0.473656 0.70
6 1.11032 0.441305 2.52 2.05
7 1.27879 0.405824 3.15 0.58
8 1.53186 0.429636 3.57 0.93
9 1.89939 0.417501 4.55 1.28
10 1.32292 0.432035 3.06 -1.96
12 1.14005 0.348412 3.27
13 0.597457 0.368628 1.62 -1.68
14 1.14412 0.345941 3.31 1.70
15 0.702531 0.391139 1.80 -1.27
16 1.28736 0.345592 3.73 1.69
17 1.02784 0.402238 2.56 -0.73
18 2.18526 0.380910 5.74 3.00
19 2.01136 0.377817 5.32 -0.48
21 0.175373E-01 0.344453 0.05
22 -0.289134 0.367201 -0.79 -0.92
23 -0.526257E-01 0.341324 -0.15 0.72
24 -0.434003 0.428302 -1.01 -0.96
25 0.387543 0.330168 1.17 2.12
26 0.841710 0.368787 2.28 1.46
27 0.511368 0.343202 1.49 -1.02
28 0.700526 0.368727 1.90 0.58
30 0.268886 0.335729 0.80
31 0.157120 0.373651 0.42 -0.34
32 0.783535 0.337129 2.32 1.88
33 0.354103 0.377379 0.94 -1.31
34 0.307839 0.330902 0.93 -0.15
35 0.249013 0.370579 0.67 -0.19
36 0.664194 0.350968 1.89 1.28
37 0.149700 0.397414 0.38 -1.45
39 -0.200152 0.382730 -0.52
40 0.777429 0.390843 1.99 2.56
41 0.642173 0.359364 1.79 -0.38
42 0.763547 0.349466 2.18 0.41
43 0.927278 0.410985 2.26 0.45
44 0.247100 0.389203 0.63 -1.74
45 1.14578 0.437099 2.62 2.13
46 0.871837 0.361796 2.41 -0.68
48 -0.570704E-01 0.274859 -0.21
49 -0.117886 0.283593 -0.42 -0.31
51 0.342601 0.396471 0.86
52 0.543503 0.361774 1.50 0.64
53 0.624197 0.331368 1.88 0.36
54 0.742765 0.347554 2.14 0.58
55 0.737851 0.339095 2.18 -0.02
56 0.605649 0.350403 1.73 -0.60
58 0.354025E-01 0.271534 0.13
59 -0.165697 0.282213 -0.59 -0.81
60 0.162915 0.266181 0.61 1.35
61 -0.227290 0.302158 -0.75 -1.47
62 0.103484 0.269090 0.38 1.23
63 0.759757E-01 0.318637 0.24 -0.10
64 0.152135 0.298886 0.51 0.24
65 0.267266 0.292245 0.91 0.40
67 -0.357367 0.262766 -1.36
68 -0.329278 0.277672 -1.19 0.11
69 -0.998269E-01 0.258377 -0.39 0.93
70 -0.283057 0.335977 -0.84 -0.59
71 0.141806 0.250313 0.57 1.39
72 -0.422662E-03 0.282444 0.00 -0.59
73 0.636443E-01 0.258561 0.25 0.26
74 0.649604E-01 0.281405 0.23 0.01
76 -0.212728 0.256526 -0.83
77 -0.137410E-01 0.288545 -0.05 0.81
78 0.140028 0.258659 0.54 0.62
79 -0.357449E-01 0.287487 -0.12 -0.72
80 0.150568 0.253528 0.59 0.79
81 0.269930 0.283689 0.95 0.51
82 0.168932 0.270275 0.63 -0.40
83 0.264377E-01 0.311598 0.08 -0.50
85 -0.280678 0.307914 -0.91
86 0.120227 0.308870 0.39 1.32
87 0.119775E-02 0.285389 0.00 -0.42
88 0.635952E-01 0.274969 0.23 0.26
89 0.268078 0.326479 0.82 0.71
90 -0.284451E-01 0.302937 -0.09 -0.95
91 -0.485748E-01 0.351411 -0.14 -0.06
92 0.394832 0.283014 1.40 1.38
23 Tr.AFDEL
94 -1.95463 0.472443 -4.14
95 -1.36488 0.404931 -3.37 1.28
96 0.222089 0.402217 0.55 6.03
97 1.52619 0.400590 3.81 12.68
99 0.704876 0.405446 1.74
100 -0.676428 0.407123 -1.66 -14.63
101 -0.314185 0.411014 -0.76 1.14
102 -0.297948 0.409026 -0.73 0.13
104 -1.22855 0.392360 -3.13
105 -0.480049 0.324478 -1.48 2.00
106 -0.428373 0.320747 -1.34 0.22
107 0.621976E-01 0.319517 0.19 5.24
109 -0.731827 0.325190 -2.25
110 -0.568875 0.326497 -1.74 1.87
111 -0.104518 0.335818 -0.31 1.72
112 0.152659 0.334718 0.46 2.30
22 Tr.K
114 -0.563157 0.694946E-01 -8.10
116 0.138333 0.620933E-01 2.23
21 Tr.SEX
118 1.91649 0.480323E-01 39.90
120 1.17203 0.439993E-01 26.64
20 Trait
121 15.0685 0.512789 29.39
122 6.49077 0.333321 19.47 -17.88
25 Tr.IND 10654 effects fitted
26 Tr.DAM 10654 effects fitted
SLOPES FOR LOG(ABS(RES)) on LOG(PV) for Section 1
-0.41 0.74
51 possible outliers: see .res file
Finished: Tue Dec 25 10:59:58 2001 LogL Converged
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