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

Daniel Brewer daniel.brewer at icr.ac.uk
Wed Apr 22 17:42:11 CEST 2009


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

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)

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


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.

This e-mail message is confidential and for use by the a...{{dropped:2}}

More information about the Bioconductor mailing list