We continue to run experiments like the ones I asked about a few months ago (DESeq design question). One of the latest comparisons is between two different compounds in the same cell line. We would like to find those genes that behave differently when comparing between the two. If I follow the suggested logic for figuring out the contrast to use, I get the following:
(cell1 compound 1 - cell 1 control) - (cell1 compound 2 - cell 1 control) ?= 0 <=> (cell1 compound1) - (cell1 compound2) ?=0 results(dds, contrast=list("cellc1.compoundc1","cellc1.compound2"))
However, this seems to give me genes that behave similarly as well, i.e. they are down (or up) in both treated sets of samples.
To elaborate more on what I mean, the two compounds are thought to essentially do the same thing albeit at different strengths of effect. How can I show this best and/or how can I find any genes that behave differently from the other genes. An extreme example for the latter would be that gene X is unregulated when treated with compound 1 but down regulated with compound 2.