Hello, I have a question regarding to outputs from a DESeq2 analysis that I wasn't sure if it is normal. Briefly, I have an RNA-seq experiment analyzed by Salmon, imported into R by tximeta, and analyzed by DESeq2. After prefiltering, my DESeqDataset had 76015 transcripts.
keep <- rowSums(counts(dds)) >= 10 # genes with at least 10 reads across all samples dds <- dds[keep, ] dim(dds) # 76015 20
After running DESeq2, the raw pvalue has a distribution looks like below
And the adjusted p-value looks like below (I have to log transform the y-axis in order to show that I do have some padj near 0)
I wonder if this looks possible or indicates any serious issues. BTW there are about ~14000 NA in padj, which should not be the sole reason for this raw pvalue distribution.