Predict GxE for XFA

From: Ky Mathews <Ky.Mathews_at_CSIRO.AU>
Date: Wed, 9 Aug 2006 14:11:48 +1000

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.


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
"It is not the strongest of species that survive, nor the most
intelligent, but the one most responsive to change." - Charles Darwin
Received on Mon Aug 09 2006 - 14:11:48 EST

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