Thanks a lot Natasha, edgeR is exactly what I was looking for.
I am also a statistics beginner and I have an another question ,but I don't
know if it's correct or not: To compute BCV in edgeR, why the developers
didn't use ANOVA? I think that the MDS in edgeR is s sort  of SSB(sum of
squares between) in ANOVA.
Thank you very much.

On 13 September 2012 10:46, Natasha Sahgal <nsahgal@well.ox.ac.uk> wrote:

> 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,
> Natasha
>
>
> -----Original Message-----
> From: bioconductor-bounces@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of Vincenzo Capece
> Sent: 13 September 2012 07:53
> To: bioconductor@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
> conditions(treated,untreated)
> Example:
>                                           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.
> Regards.
>
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>
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-- 
Regards,
            Capece Vincenzo

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