[BioC] experiment design in EdgeR -- correction

Gordon K Smyth smyth at wehi.EDU.AU
Thu Oct 25 07:23:49 CEST 2012

Dear Anna,

I replied to your question below too quickly, and my advice below was too 
simple.  For better advice, see the response I made a few minutes ago to 
your later posting regarding the same experiment.

Best wishes

  On Wed, 24 Oct 2012, Gordon K Smyth wrote:

> Dear Anna,
>> Date: Tue, 23 Oct 2012 01:27:13 -0700 (PDT)
>> From: "anna [guest]" <guest at bioconductor.org>
>> To: bioconductor at r-project.org, m.nadira at yahoo.fr
>> Subject: [BioC] experiment design in EdgeR
>> Then I have the same question whether to use several paired analyses, or 
>> first a blocking analysis for each group followed by several paired 
>> analyses, or another kind of analysis for those paired experiments:
>> cells from 3 healthy patients , either treated or not with a hormone .
>> cells from 3 patients with disease D1, either treated or not with the 
>> hormone
>> cells from 3 patients with disease D2, either treated or not with the 
>> hormone.
> Just treat this is six groups, following Section 3.3.31 "Defining each 
> treatment combination as a group" in the edgeR User's Guide.
> If you can't find these sections in your User's Guide, then update the 
> current Bioconductor release.
> Best wishes
> Gordon
>> I would like to know what is wrong in the response to the hormone in 
>> patients with disease D1 and D2.
>> thank you very much,
>> anna

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