I am using Transcriptome Analysis Console (TAC) for DE testing of gene expression data and R for downstream analyses and visualization. I generated volcano plots for three separate datasets (let's call them A, B, and C), and the distribution of p values does not look uniform (there are some gaps as can be seen in the images below). Even in dataset B whose P value distribution looks good, there are no genes with -log10p around 4.
I have never seen this pattern before and I am not sure what to make out of it. What do you think this indicates? Perhaps poor quality of the data?