Re: G*E in animal model

Thanks Alastair,

I had a similar idea, but didn't know if it would be an acceptable test of
G*E. Your suggestion has encouraged me to plough ahead with this approach.

Allt he best,

Rob

At 10:04 AM 20/07/2005 +0100, you wrote:
>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

............................................................................
............................
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 Wed Jul 21 2005 - 11:10:44 EST