I am working with two subtypes of immune cells. For each of them I have two states - naive and activated. I am interested in the differential expression between these states in each cell type. I'll call these comparisons Contrast A and Contrast B. I am also interested to find out what is the difference between these two contrasts, i.e. to "compare the comparisons" (an illustration can be found here: http://bit.ly/1A1o6ZP). How can I model such comparison in edgeR?
My sample metadata looks like this: http://bit.ly/1EBZ9Kv
Modelling contrasts A and B is trivial (e.g. exactTest(d, pair=c("A-n", "A-act")). Can you write down the model for the "comparison of the comparisons"?