Hi, I am running a DESeq2 analysis for some data. I have two different conditions in my data which should have identical RNA-seq at day 0 (I am doing a time course experiment). However, when I run them through DESeq2, I get a hill-shaped pvalue distribution (plotting non-adjusted p-values), shown below. Do you have any idea why this might be?

In my experience, that is relatively easily fixed by using svaseq from the sva package to generate some surrogate variables to account for unobserved variability.