I want to run a differential expression experiment with DEseq2, however I am a little confused regarding how to set up the formula. I have matched tumor/normal pairs and I want to contrast that to a third clinical variable (see table below).
Sample Tissue Clinical_Status
SampleA Tumor X
SampleA Normal X
SampleB Tumor Y
SampleB Normal Y
The biological question is: "Are there Differentially expressed genes in tumor samples according to clinical status?"
To answer this I could remove the normal samples all together in which case the design formula would be this: design = ~ Clinical_Status
However This does not seem optimal as I would have no idea if the genes would be DE in the normals as well and as such should be ignored. I could run the test again (for normals) and remove those DE genes from the original test however I believe there would be a multiple testing problem there.
I am thinking there is a way to test what I want all at once and design should be something like this: design = ~ Sample + Clinical_Status + Tissue:Clinical_Status
However I am not 100% sure, any help would be appreciated. apologies for the naivety of the question.