[BioC] DESeq2 comparison of treatment in two conditions

Kauer Max maximilian.kauer at ccri.at
Thu Mar 6 12:38:40 CET 2014

I have a RNAseq dataset with this design:

               condition       treatment
sample1        A                 treat
sample2        A                 treat
sample3        A                 con
sample4        A                 con
sample5        B                 treat
sample6        B                 treat
sample7        B                 con
sample8        B                 con

so there are two conditions and within each condition treatment and control.
So far I simply compared treat vs. con within each group, so I get logFCs and
p values for A and B separately (for this I actually subsetted the dataset and used ~treatment as design)

Now I would also like compare the two conditions to see genes that respond differently to treatment in A and in B.
So my question: how do I set up the design for that?

Thanks in advance!

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