I am doing an RNA-seq analysis with DESeq2. I have 3 patients with disease (affected) and 3 healthy patients (unaffected). After following standard DESeq2 pipeline (as described here), I got my table with results and p.value column. I decided to check the distribution of p.values and here it is:
I do know that we expect to see something similar to uniform distribution, apparently we don't see it here... Does it mean that there is a problem with the data or an experiment design (I used simple formula, which was taking into account genders of the patients: ~ Gender + Condition)?