Re: G*E in animal model

Rob,

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

0
Trait 0 US
0.1
0.01 0.1 #or better starting values

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

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.

Cheers,

Alastair

Alastair J Wilson PhD
Postdoctoral Research Fellow

Alastair.Wilson_at_ed.ac.uk

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>
To: <ASREML-L_at_AGRIC.NSW.GOV.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
> GENERAT !A
> ENV 2
> CE_PN
> 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
> http://www.bees.unsw.edu.au/research/groups/brookslab/brookslab.html
Received on Tue Jul 20 2005 - 10:04:45 EST