[BioC] Differential expresson in more than 2 samples using NGS?

Gordon K Smyth smyth at wehi.EDU.AU
Thu Aug 26 03:04:00 CEST 2010

Dear Xiaohui,


Suppose you want to show that a particular gene is up-regulated in 
condition 3 relativve to conditions 1, 2 and 4.  It seems to me that you 
have to compare conditions 3 vs 1, 3 vs 2 and 3 vs 4, in order to 
establish this.

Best wishes

On Wed, 25 Aug 2010, Xiaohui Wu wrote:

> 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
> ·¢¼þÈË£º Gordon K Smyth
> ·¢ËÍʱ¼ä£º 2010-08-25  19:56:19
> ÊÕ¼þÈË£º Bioconductor mailing list
> ³­ËÍ£º Wu, Xiaohui Ms.
> Ö÷Ì⣺ [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 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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