(disclosure: first question on Biostars, my apologies if I go against any rules!)
My RNA seq data consists of one cell type extracted from three tissues (A, B, C) from two groups (diseased and controls).
sample breakdown
Disease_TissueA: 17
Disease_TissueB: 18
Controls_TissueC: 15
I have three questions I want to ask
1) differences between disease_tissueA and controls_tissueC
2) differences between disease_tissueB and controls_tissueC
3) overlap between questions 1 and 2, ie. disease vs controls (regardless of disease tissue of origin)
I'm using sleuth for differential gene expression analysis and have already performed the first two models and obtained two gene lists. Now, my question is how to appropriately answer question 3. At first, I just overlapped the two gene lists to see how many overlapped, but I'm wondering if I should run a third model just disease vs controls or if there is a more sophisticated way of approaching this. Any advice?
Thanks in advance.
