[BioC] Best way to find genes that represent a group

[Daniel Brewer]

Hello,

I have five groups of samples that I have microarray data for and I
would like to know what genes make that group distinct from the other
groups.

The initial approach I took was to use limma to do a comparison between
one group and the rest, for example:

design1 <- model.matrix(~pData(alignedSetlur)$group ==1)
fit <- lmFit(alignedSetlur,design=design1)
fitone <- eBayes(fit)
topTable(fitone,coef=2,n=Inf,p.value=0.05)

I did this for each group, but I found that there was a large amount of
overlap between the significant genes in one group and another (over 50%
in some cases) and this doesn't seem correct.

What is the best way to answer this sort of question?  Some sort of
multivariate analysis or PCA?

Many thanks

Dan

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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