Re: contrasts in ASREML

From: Arthur Gilmour <arthur.gilmour_at_CARGOVALE.COM.AU>
Date: Thu, 3 Sep 2009 08:21:56 +1000

Dear Bart,

The reported effect is the regression implicit in the contrast.

Assuming you wrote the contrast as 0 1 0 -1
the regression is Sigma XY /Sigma XX = (.385 - .975) / 2 = -.295

Now if you have unbalanced data and non-orthogonal contrasts,
the reported effect will be as in the context of the full model,
but the Wald F statistic will test the contrast as the incremental
effect as it is added in the model. So, this is another reason
the fitted contrast may not reflect the simple contrast.

But I suspect the former applies in your case.

On Wed, 2009-09-02 at 10:00 +0200, Ducro, Bart wrote:
> Dear Arthur and others,
> We have a question about the estimation of contrasts. If you look at
> the solutions of the fixed effects (in the .sln file) from a mixed
> model analysis, we get the following results:
> code estimate s.e.
> 99 0.000 0.00
> 10 0.385 0.227
> 11 0.764 0.207
> 12 0.975 0.226
> Based on these solutions we would expect the following contrasts
> between classes 10 and 12 of about -0.59
> If we estimate the contrast using !CONTRAST we get -0.297 (with s.e.
> of 0.089).
> Do we overlook something?
> Thanks in Advance,
> Henk Bovenhuis and Bart Ducro
> Wageningen University
> The Netherlands
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Best Wishes,
Arthur Gilmour
Adjunct Professor
School of Computing and Mathematics
Charles Sturt University
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Received on Fri Sep 03 2009 - 08:21:56 EST

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