[BioC] EdgeR: paired samples together with independant samples

[Gordon K Smyth]

Dear Anna,

You are right to recognise that the analysis of this sort of design is 
more complex than many other experiments, because it includes comparisons 
both within and between patients.  I have included a new section in the 
edgeR User's Guide based on your experiment that describes the analysis. 
This will appear in the official release of edgeR in a couple of days. 
In the meantime, see pages 31-33 of:

   http://bioinf.wehi.edu.au/software/edgeR/edgeRUsersGuide.pdf

Best wishes
Gordon

> Date: Tue, 23 Oct 2012 06:37:44 -0700 (PDT)
> From: "anna [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, m.nadira at yahoo.fr
> Subject: [BioC] EdgeR: paired samples together with independant
> 	samples
>
>
> Hello,
> I am using EdgeR to analyse my RNAseq data.
>
> I have:
>
> 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.
>
> I would like to know what is wrong in the response to the hormone in 
> patients with disease D1 and D2.
>
> I don't know how to combine paired comparisons, with pairwise 
> comparisons, in a unique glm analysis.
>
> 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
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>

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