Re: Models with parents and heterotic groups

From: Arthur Gilmour <arthur.gilmour_at_CARGOVALE.COM.AU>
Date: Sat, 24 Oct 2009 13:02:22 +1100

Dear Chloe,

   The model should be
Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
!r GrHet1 and(GrHet2) Parent1 and(Parent2)

where Parent1 and Parent2 are code the same genotypes in the same
order, and GrHet1 and GrHet2 code the same heterotic groups in the
same order.

The .sln file will then contain a set of effects for Environment,
a mu effect, a set of effects for GrHet1
and a set of effects for Parent1

predict Parent1 !PRESENT Parent1 GrHet1
will then calculate an overall mean being mu + average of Environment
and combine this with each of the Parent effects and the associated
GrHet effect, to produce a list of Parent solutions.

The predicted values (Yhat) in the .yht file calculated from the model
desgn matrix. So for example, for an observation in Env 3 being the

progeny of Parent 5 (Group 1) and Perent 10 (Group 3),
the Yhat value is
   mu + 3rd environment effect + 5th Parent effect + 1st Group effect +
10th Parent effect + 3rd group effect.

If you wanted to predict the progeny of Parent 5 and Parent 11 (not
being a combination present in the data), we may need to experiment.

predict Parent1 5 Parent2 11 GrHet1 1 GrHet2 3 !PARALLEL Parent1,
 Parent2 GrHet1 GrHet2

might do the trick.

On Fri, 2009-10-23 at 14:02 +0100, Chloe wrote:
> The main problem I have with the following model you proposed is that
> I 'm not able to compute the predicted values in the .pvs neither in
> the .yht from the .sln .
> Recolte !BINOMIAL !LOGIT !TOTAL Plantes ~ mu Environnement,
> !r GrHet1 and(GrHet2) Parent1 and Parent2
> predict Parent1 !PRESENT Parent1 GrHet1
> What are the effects to sum to get the .pvs file from the .sln?

Best Wishes,
Arthur Gilmour
Adjunct Professor
School of Computing and Mathematics
Charles Sturt University
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Received on Sun Oct 24 2009 - 13:02:22 EST

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