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<div class="moz-cite-prefix">Hi Lennart,<br>
<br>
If ProbABEL is using the same 'two steps score test' as it was in
the first version (section 'Two-step score test for association'
in ProbABEL paper <a class="moz-txt-link-freetext" href="http://www.biomedcentral.com/1471-2105/11/134">http://www.biomedcentral.com/1471-2105/11/134</a>)
then, I guess, the GxE term can be included in the model and run
in mmscore. It only should be assured that the interaction term
goes to the second step (run the model trait_residuals ~ snp +
snp*E in mmscore). Otherwise, it may results in false positives.<br>
<br>
Actually, in the first paragraph of section 'Two-step score test
for association' of ProbABEL paper, it is written that "design
matrix may include not only the main SNP effect, but e.g. SNP by
environment interaction terms". So, I would include it and look
what will happen.<br>
<br>
P.S. IMHO it is interesting to run this scenario briefly in a
small simulation study.<br>
<br>
Best,<br>
Maksim<br>
<br>
<br>
<br>
On 17/10/2014 21:54, L.C. Karssen wrote:<br>
</div>
<blockquote cite="mid:54412DA5.2070309@karssen.org" type="cite">
<pre wrap="">Dear list,
There is a question on the forum [1] that I'm not sure how to answer.
The user wants to run mmscore and test for interactions. There is
nothing in ProbABEL that prevents her from doing that. However, in the
manual we state:
"Though technically --mmscore allows for inclusion of multiple
covariates, these should be kept to minimum as this is a score test. We
suggest that any covariates explaining an essential proportion of
variance should be fit as part of GenABEL’s polygenic procedure."
Does this also apply for interactions between SNP and a covariate? If so
we should produce an error message when both options are specified.
What is the proper way to deal with interactions and mmscore?
Best,
Lennart.
[1] <a class="moz-txt-link-freetext" href="http://forum.genabel.org/viewtopic.php?f=10&t=896">http://forum.genabel.org/viewtopic.php?f=10&t=896</a>
</pre>
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