Dear Andrew
One alternative is to treat SNP as random effects, and test its significance with likelihood ratio test.
I think ASReml can do this, e.g. Height ~ mu HYS Age !r SNP ANIMAL
Hong
---------[ 받은 메일 내용 ]----------
제목 : Order of fitting fixed effects
날짜 : Mon, 27 Jul 2009 16:22:25 +0100
보낸이 : "Clempson, Andrew Martin" <aclempson@RVC.AC.UK>
받는이 : ASREML-L@DPI.NSW.GOV.AU
Dear All,
I am looking for some advice on determining the order in which fixed
effects should be fitted in an animal model.
I am currently carrying out association studies between SNPs and growth
in cows. My fixed effects include herd-year-season (HYS), covariate of
Age, and the SNP, and a random effect of 'Animal'. The model is
currently arranged in the following order -
Height ~ mu HYS Age SNP !r ANIMAL
I have found that if I change the order in which the fixed effects are
fitted, the results differ. After checking various papers, it appears
that some have fitted the SNP first, whereas others fit the SNP at the
end.
I would be very grateful for any clarification,
Kind Regards
Andrew
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