[BioC] EdgeR: paired samples together with independant samples

[anna [guest]]

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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