[BioC] DESeq2 comparison of treatment in two conditions
Kauer Max
maximilian.kauer at ccri.at
Thu Mar 6 12:38:40 CET 2014
Hi,
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!
max
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