[BioC] experiment design in EdgeR

[Gordon K Smyth]

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
>
>
> Hello,
> I am using EdgeR to analyse RNAseq data.
> I would like to know whether I should use several paired analyses or a blocking analysis for this paired experiment:
> I have cells from3 patients. For each patient, I have 3 conditions: cells were either Non treated, treated with drug 1, or treated with drug 2.
> I would like to know what each drug does, and the difference between them.
> I have a doubt because in this case a block would be one patient, so cells are exactly the same.

Thsi is a blocked design, described in Section 3.4.2 "Blocking" in the 
edgeR User's Guide.

> 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
>
> -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base

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