Hi, I have a question regarding the DESeq2 design of an analysis I've been wanting to try.
Say in our experiment we have 4 conditions:
-sample with transfected gene A
-sample with transfected gene B
-sample with both transfected genes A + B together
The assumption is that when the 2 genes are expressed in parallel they activate a unique mechanism, which is not normally activated when each gene is expressed individually.
Thus, if the research aim is to find the differential gene expression induced by ONLY the combination of transfected genes A + B without including differentially expressed genes induced by either gene A or B individually, what would be the best way to go about it?
The simplest and most obvious way to me would be to do the following contrasts:
-transfected gene A vs control
-transfected gene B vs control
-transfected genes A + B vs control
Then I keep only the differential genes in the "transfected genes A + B vs control" contrast that are not also found in the results of the other two contrasts.
The issue is that I would be compromising the FDR control of the DESeq2 gene results by arbitrarily removing genes from the list because they are found in another list. Is there another way of doing this analysis with a different design in DESeq2 or is this the only way?
Thank you in advance.