[BioC] DESeq - working with more than 2 conditions
anders at embl.de
Thu Sep 13 11:31:30 CEST 2012
> I have a question about DESeq: DESeq works fine if I have 2
> treated untreated
> ENSMUSG00000000001 193 254
> ENSMUSG00000000003 0 0
Well, this is not a great example, as your conditions are not
replicated, but, of course, that was not your question.
> 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?
Of course, there are plenty of methods to work with more than two
conditions, by usign generalized linear models (GLMs).
What you need to do depends on the question you want to ask. For two
conditions, there is one obvious question, namely: Which genes are
significantly stronger in condition A, and which ones are stronger in
In your case, what would the question be?
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