Gene expression - finding DE genes

[LConley]

Hi

I am working with Solexa RNAseq where I want to compare 2 classes (e.g. normal vs sick) with 3 biological samples in each (e.g. 3 patients) and find differentially expressed genes/tags between the 2 classes.

Does anybody have suggestions on which test/program (preferable freeware) or online tool that I can use? Perhaps an R package?

So far I have looked into SAGEBetaBin:
http://www.vision.ime.usp.br/~rvencio/SAGEbetaBin/
and it seemed to be working fine a few months ago, but now I have troubles submitting.

Thanks,
Lene

[florian]

hey,

you might wqant to try the "edgeR" bioconductor package.

http://www.bioconductor.org/packages/bioc/html/edgeR.html

works well for me...

cheers, florian

[LConley]

hey,

you might wqant to try the "edgeR" bioconductor package.

http://www.bioconductor.org/packages/bioc/html/edgeR.html

works well for me...

cheers, florian

Thanks - I will look into that