[BioC] DESeq - working with more than 2 conditions

[Simon Anders]

Dear Vincenzo

> I have a question about DESeq: DESeq works fine if I have 2
> conditions(treated,untreated)
> Example:
>                                           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 
condition B?

In your case, what would the question be?

   Simon