Re: multivariate genetic analysis using SPLUS asreml

From: <brian.cullis_at_DPI.NSW.GOV.AU>
Date: Thu, 18 Oct 2007 08:10:32 +1000

Dear Jarrod and Alastair,
Thanks for the advice. Changing ~1 to ~trait doesn?t seem
to do anything but changing the G structure for Dam and Cage
does change the estimates. Unfortunately, it does not
eliminate the scale problem. Calculating the heritabilities
using a single trait model gives consistent answers (no
scale effect) that are essentially the same as those from a
standard anova analysis. I know that there is nothing
fundamentally wrong with the data as a manova analysis gives
sensible results. It is not clear if I am making an error
in my coding or there is a problem with the program itself.
Unhappily the splus version seems to be poorly supported and
I am on the verge of giving up on it.
Thanks for all your help.

Just a couple of things, though I have not paid great attention to the

1. the splus version is not poorly supported, just not heavily used and so
there may be bugs as there always are in any software
2. The R interface is excellent to use. I would strongly recommend
ASReml-R. David Butler now has it pretty much uptodate with the most
recent ASReml stand-alone. Of course the advantage is that R is free & has
much more usage (ie most of NSWDPI & others and myself are constantly
testing it, whereas I dont know too many who use Splus version)
3. gamma and component are the same for the model you fit as there is no
overall scale parameter (see manual where this is described in detail)
4. Jarrod's model is the more sensible model. it is very important to
correctly model sources of variation at all levels in multivariate data
5. I can't see what the issue is with scaling. So called MANOVA and ASReml
model as per Jarrod should produce the same results. It may be convergence
with scaling, it may be something else. I would need the data to properly


Brian Cullis
Research Leader, Biometrics &
Principal Research Scientist
NSW Department of Primary Industries
Wagga Wagga Agricultural Institute

Faculty of Agriculture, Food & Natural Resources
The University of Sydney

Phone: 61 2 6938 1855
Fax: 61 2 6938 1809
Mobile: 0439 448 591
Received on Mon Oct 18 2007 - 08:10:32 EST

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