[BioC] interaction effect (4x2)
seb at gerega.net
Fri Feb 29 00:05:29 CET 2008
Thanks for your reply James,
James W. MacDonald wrote:
> Well, with 4 groups and 2 treatments I get 6 total interactions. Are
> the three you are testing here the interesting interactions?
I guess I am interested in all 6 interactions. How would I go about
looking at them all?
>> So far, from looking at expression profiles, I don't seem to be
>> picking out interesting genes....
> Interesting defined how? The genes you get aren't a priori genes you
> want to see? Or you aren't getting any significant genes?
The reason I said that was initially I accidentally performed the
analysis without applying the contrast:
interDesign = model.matrix(~factor(sDrug) * factor(sGroup))
interFit = lmFit(lumi.N.P, interDesign)
interFit = eBayes(interFit)
interDTest = decideTests(interFit, method="nestedF",
which(abs(interDTest[,6]) == 1 | abs(interDTest[,7]) == 1 |
abs(interDTest[,8]) == 1)
And the genes I identified that way were interesting to me, based on a
quick glance at expression profiles. Then I realised I should have
applied a contrast.
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