Thank you in advance for your feedback and suggestions.
I am currently doing some RNA-Seq analysis using DESeq2 and I have noticed that when I plot a histogram of my raw pvalues, I notice most of the genes are at p value of 1. My histogram looks very similar to scenario D of the following link http://varianceexplained.org/statistics/interpreting-pvalue-histogram/. My first question is why would this be happening? My first thought was the presence of lowly expressed genes, however, after looking over the guide for DESeq2, it mentions that in the analysis lowly expressed genes are filtered out of the analysis. So any feedback on this is appreciated. In addition, I am making several comparisons and only one comparison results in a p value histogram similar to scenario A of the link. My second question is why would some comparisons result in anticonservative values (scenario A) and in the same analysis other comparisons would result in conservative p values (scenario D).