Re: Order of fitting fixed effects

From: Peter Thomson <petert_at_CAMDEN.USYD.EDU.AU>
Date: Tue, 28 Jul 2009 07:02:57 +1000

Hi Andrew,


If you include the option !FCON in the data file specification line, it
will return conditional F-tests on all the fixed effects, i.e. adjusting
for all the other fixed effects, as opposed to the default sequential
F-tests. I think that is what you are after. I think it also makes
sense to assess the SNP effect, after adjusting for the other term in
the model.






Associate Professor Peter Thomson
ReproGen - Advanced Technologies in Animal Genetics and Reproduction
Faculty of Veterinary Science, University of Sydney
Private Bag 4003 Narellan NSW 2567 (425 Werombi Road, Camden NSW 2570)

Tel: +61 2 9351 1654 Fax: +61 2 9351 1693

e-mail: <>


From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On
Behalf Of Clempson, Andrew Martin
Sent: Tuesday, 28 July 2009 1:22 AM
Subject: Order of fitting fixed effects


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


I would be very grateful for any clarification,

Kind Regards




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Received on Wed Jul 28 2009 - 07:02:57 EST

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