Re: Predict GxE for XFA

From: Dr Ian DeLacy <i.delacy_at_UQ.EDU.AU>
Date: Wed, 9 Aug 2006 20:11:18 +1000

The mu is not the mean but a multiple regression constant and is almost never
the mean. You can only make mu the mean if you set all the fixed effects to
sum to zero a very troublsome thing in what you are really meaning to do.
I totally avoid the problem by fitting a model such as
... g gy gl gyl if I want overall cfs among entries over all data
... gl gyl if I want to cf the performance of entries in each location
averaged over years
... gy gyl if I want to cf the performance of entries over years averaged
over locations.
I think it is best to live with all these values summing to zero then trying
to rescale them
If you want to give breeders or others a feeling for the values (height being
a case where they are interested) predict overall mean or site means of year
means using the BLUEs.

Quoting Ky Mathews <Ky.Mathews_at_CSIRO.AU>:

> Dear ASREML-colleagues,
> I'm fitting an factor analytic (XFA2) model to a multi-environment trial
> for wheat data.
> I want to predict the GxE BLUPs an use the following code
> predict env.gen !only xfa(env,2).gen
> This gives me BLUP estimates but we would like them to be on the same
> scale as the measurements, i.e. I obtain mu from the .sln file and add
> it to the BLUP estimates.Thus, we're not changing any ranking cos we're
> simply adding the same constant to all BLUPs.
> Is this correct? (I thought so!)
> But... in recent analyses of height data I see that the predicted values
> for some envs are well below what was actually observed.
> I know that BLUPs get shrunk back the mean (mu, I assume?), but is there
> a way to adding back in the environment main effect? I suspect that this
> may not be a sensible thing to do as environments are fixed, so we'd
> have a BLUE + BLUP which does not equal a BLUP!
> Any suggestions/advice would be much appreciated.
> Thanks
> Ky
> Dr Ky L Mathews
> CSIRO Plant Industry
> Queensland Bioscience Precinct
> 306 Carmody Road
> St Lucia QLD 4067 Australia
> Ph: +61 7 3214 2255
> Fax: + 61 7 3214 2920
> Email:
> "It is not the strongest of species that survive, nor the most
> intelligent, but the one most responsive to change." - Charles Darwin

Dr Ian DeLacy
Lecturer in Genetics and Plant Breeding
School of Land and Food Sciences
University of Queensland
Brisbane, 4072
Phone +61 (7) 3365 2833
E Mail
Received on Mon Aug 09 2006 - 20:11:18 EST

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