Entering edit mode
Dear Xiaohui,
I suspect you mean more than 2 groups or conditions rather than 2
samples.
edgeR already handles any number of groups. If you want to find genes
highly expressed in one condition but not in the others, surely you
need
to make pairwise comparisons between the conditions, and that is
exactly
what edgeR does.
In the next month, we will be adding linear model capabilities to
edgeR,
but it sounds to me as if the package will already address your
problem as
it is.
Best wishes
Gordon
> Date: Tue, 24 Aug 2010 12:49:08 -0400
> From: "Xiaohui Wu" <wux3 at="" muohio.edu="">
> To: "bioconductor" <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] Differential expresson in more than 2 samples using
> NGS?
>
> Hi all,
>
>
> I have about 30 libraries of SBS data (millions of 20nt tags) to
analyze
> the differences between or among different libraries, and lots of
these
> tags are in intergenic regions.
>
> For gene regions, I think I can use DESeq or EdgeR to analyze the DE
> genes. But it seems that DESeq or EdgeR can only deal with two
samples,
> is there any package to compare multiple samples one time. For
example,
> to find genes expressed highly in one or some libraries but not in
other
> libs.
>
> But for intergenic tags, I think first I should use some peak
detection
> package to find peak in intergenic, then treat these peaks as genes
to
> find DE regions.
>
> Is there any peak detection package for NGS? and package for DE
analysis
> among multiple libs?
>
> Thank you!
>
> Regards,
> Xiaohui
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