our group has been using the function DESeq of the library DESeq2 to perform differential expression analysis. We notice than some features get a p-value much smaller than the machine epsilon. There are two points that we find difficult to understand.
1. How are these functions generating the p-values, especially those that are smaller than the epsilon of the machine?
2. How meaningful is a comparison of p-values that are negligibly small, say 10^(-250) and 10^(-251)?
We would deeply appreciate any help for the understanding of these questions.