[BioC] interaction effect (4x2)

Sebastien Gerega 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", 
adjust.method="fdr", p.value=0.05)
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.
thanks again,

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