Dear colleagues,
I tried to fit some large animals models including genetic groups and compared them with models without genetic groups. I carefully checked that all unknown animals in the pedigree file were assigned to a genetic group.
In the models with genetic groups I found very high SE for estimates for the effects of animal (derived from *.sln files) compared to the estimated genetic variance. As an example, I found a genetic variance of 0.66 whereas the SE of
an animal was 1.472, which seems to be much too high.
What might be wrong here ?
To test the genetic groups I compared the results of a very small example (10 animals, two sires, unknown dams) with and without genetic groups (group.as vs. nogroup.as, see below). Also here I ended with different results.
In the no-group version I found an estimate for A of -0.3105 (SE 0.6207) whereas it was -0.500 (SE 1.905) in the version with genetic groups. I expected the same results when all unknown animals are assigned to the same genetic group.
I am not quite sure if the differences of these small exemples are caused by the size of the data or by mistakes in the *.as files.
Best regards,
Erwin Koenen
NOGROUP.DAT / GROUP.DAT
1 3.5
2 5.5
3 4.5
4 5.0
5 3.0
6 4.0
7 6.0
8 5.0
9 6.0
10 4.5
NOGROUP.PED
A 0 0
B 0 0
1 A 0
2 A 0
3 A 0
4 A 0
5 A 0
6 B 0
7 B 0
8 B 0
9 B 0
10 B 0
GROUP.PED
C 0 0
A C C
B C C
1 A C
2 A C
3 A C
4 A C
5 A C
6 B C
7 B C
8 B C
9 B C
10 B C
NOGROUP.AS
WITHOUT GENETIC GROUPS
animal !P
y
nogroup.ped !ALPHA !MAKE
nogroup.dat !MAXITER=20
y ~ mu !r animal
GROUP.AS
WITH GENETIC GROUPS
animal !P
y
group.ped !ALPHA !GROUPS 1 !MAKE
group.dat !MAXITER=20
y ~ mu !r animal
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