[BioC] DESeq and contrasts

[Gordon K Smyth]

Dear Joshua,

edgeR does exactly this.  It has the ability to fit any designed 
experiment with any number of factors, and has an easy interface to 
extract any contrast from such a fit.  See page 17 of the edgeR user's 
guide for a very simple example of the use of a contrast:

http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

Best wishes
Gordon

> Date: Tue, 19 Jun 2012 15:57:44 -0600
> From: Joshua Udall <jaudall at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] DESeq and contrasts
>
> Hello all,
>
> Was there any additional discussion about investigating contrasts of
> multifactor designs within DESeq?  I saw this thread:
> http://article.gmane.org/gmane.science.biology.informatics.conductor/40048/match=deseq+contrast
>
> but no response was posted to the list.  I am essentially looking for the
> same guidance (R syntax within DESeq for contrasts and interactions).
>
> Thanks.
> Joshua Udall

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