[BioC] DESeq - working with more than 2 conditions

Natasha Sahgal nsahgal at well.ox.ac.uk
Thu Sep 13 10:46:27 CEST 2012

Dear Vincenzo,

You could try to use the edgeR package (and the glm method within it).
Also, if I am not mistaken, you could use DESeq but you have to use the glm method there. 

Hope that helps,

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Vincenzo Capece
Sent: 13 September 2012 07:53
To: bioconductor at r-project.org
Subject: [BioC] DESeq - working with more than 2 conditions

Dear all,
I am a R beginner and I hope you can help me.
I have a question about DESeq: DESeq works fine if I have 2
                                          treated   untreated
ENSMUSG00000000001      193     254
ENSMUSG00000000003      0       0
ENSMUSG00000000028      10      13
ENSMUSG00000000031      0       4
ENSMUSG00000000037      8       9
ENSMUSG00000000049      6       8

but if I have data about more than two conditions, for instance 1-month-treated,3-months-treatead, 6-months-treated,untreated, can I use DESeq? If not, Which R package (if it exists)do you suggest to use?

Thanks in advance.

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