Hello everyone, here's my question:
I have three datasets of RNA-seq data and WES of cases and controls of the same disease. After stratifying the cases in all three datasets based on the presence or absence of deleterious mutation on a particular gene I obtain: Controls, Cases_1 and Cases_2 for all three datasets. I then perform differential expression analyses for Cases_1 vs Controls and Cases_2 vs Controls for each dataset separately.
If I select the genes I find differentially expressed in all three "Cases_2 vs Controls" analyses and do not find in all three "Cases_1 vs Controls", can I consider those as a signature for the Cases_2 group? Or should additional analyses be involved?
Thanks in advance to anyone who will answer.