Hi Gordon,

Thank you for your response. 
Yes, you are right, maybe I was unclear about the sample or condition. What I said 'one sample' means one condition with multiple replicates. Do you mean I need to compare two conditions each time using edgeR, and then make the conclusions about the final DE genes among all conditions?

Xiaohui




发件人： Gordon K Smyth 
发送时间： 2010-08-25  19:56:19 
收件人： Bioconductor mailing list 
抄送： Wu, Xiaohui Ms. 
主题： [BioC] Differential expresson in more than 2 samples using NGS? 
 
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@muohio.edu>
> To: "bioconductor" <bioconductor@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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