[BioC] experiment design in EdgeR

[anna [guest]]

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. 


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.

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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