Re: G*E in animal model

From: Alastair Wilson <Alastair.Wilson_at_ED.AC.UK>
Date: Wed, 20 Jul 2005 10:04:45 +0100


Since it looks like you have 2 environments another way to do it would be to
set it up as a two trait model with CE_PN_env1 and CE_PN_env2 as separate
traits. Adjust the data file accordingly and then the rest could look
something like...

CE_PN_env1 CE_PN_env2 ~ Trait !r Trait.Anim

1 2 1

Trait 0 US
0.01 0.1 #or better starting values

Trait.Anim 2
Trait 0 US
0.1 1 #or better starting values

This would give you a residual and additive variance for the trait in each
environmnet, plus the covariances across environments. Scaling the COVa to a
genetic correlation would let you see if rG was significantly les sthan 1
(one way to define GxE). If each animal is only measured in one environment
or the other then the residual covariance will be 0 but you should still
estimate the additive covariance.



Alastair J Wilson PhD
Postdoctoral Research Fellow

tel. 0131 6507287

Institute of Evolutionary Biology
School of Biological Sciences
The University of Edinburgh
Ashworth Laboratories
The King's Buildings
West Mains Road
Edinburgh EH9 3JT, UK

----- Original Message -----
From: "Rob Brooks" <rob.brooks_at_UNSW.EDU.AU>
Sent: Wednesday, July 20, 2005 2:05 AM
Subject: G*E in animal model

> Dear ASREMLers
> I have a general and a specific query. Generally, I have enormous trouble
> designing the G and R structure lines of my ASREML jobs. Unfortunately I
> am
> just not well enough schooled in thinking about these problems, but I find
> I have to really bang my head agains the wall to figure out how to design
> these bits of my jobs. Apart from teh AREML help, Asreml cookbook and
> various web nortes from workshops, does anyone know of a good starting
> place to learn about how to set these things up properly, from first
> principles.
> More specifically the problem I have been grappling with for the last
> while
> is how to test for G*E interactions in a univariate animal model. I have
> the animal model going fine, as per the below .as file, but I cannot fit
> the Anim.ENV term. Does one specify Anim.ENV as a random effect, or is
> there another way of doing it. Irrespective, if anyone has any insights on
> how to specify the G and R structure lines in the job file, they would be
> much appreciated.
> Many thnaks,
> Rob
> Single Trait Animal Model
> Anim * !P
> Sire * !P
> Dam * !P
> SEX !A 2
> ENV 2
> am_tfd.txt !SKIP1 !ALPHA !MAKE #pedigree file
> am_tfd.txt !SKIP1
> CE_PN ~ mu ENV !r Anim
> 0 0 1
> Anim 1
> 0 0 AINV
> ............................................................................
> ............................
> School of Biological, Earth and Environmental Sciences
> The University of New South Wales
> Kensington, Sydney 2052
> NSW, Australia
> PH: +61-2-9385-2587 FAUX: +61-2-9385-1558
Received on Tue Jul 20 2005 - 10:04:45 EST

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