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Old 05-01-2009, 04:55 AM   #1
LConley
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Location: Denmark

Join Date: May 2009
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Question Gene expression - finding DE genes

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
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Old 05-01-2009, 04:59 AM   #2
florian
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hey,

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

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

works well for me...

cheers, florian
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Old 05-01-2009, 05:01 AM   #3
LConley
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Location: Denmark

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Quote:
Originally Posted by florian View Post
hey,

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

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

works well for me...

cheers, florian
Thanks - I will look into that
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