When using DESeq2, I noticed that some of my top genes have a pvalue or padj of zero. I suppose the pvalue from the Wald test is really small and it got rounded at some point when I run DESeq2, although it is a bit surprising that other packages, including limma/voom, edgeR assigned a more reasonable pvalue (e.g E-15, E-20, etc) to the same genes using the same dataset. In contrast, DESeq2 is only giving zeros for those same genes. The second lowest p-value I get (after the zeros) is E-82 for a similar logFC for the genes with p-value of zero. Given this situation, how I can use these values to generate a decent volcano plot to represent the data?. When my top genes have a value of zero, the scale of the volcano plot is just awful because the top genes are assigned -log10P values that are through the roof . Also, I would appreciate if someone could help me understand why DESeq2 doesn't provide a more reasonable p-value (I mean E-82 is a bit extreme... ). I am attaching some values from by data.Thanks!
I’ve posted here before about small pvalues before. I’m not really concerned about very small pvalues for trivially DE genes. It’s not a useful statistic for much once it’s very small. I think the useful outputs are FDR or FSR sets and posterior estimates of log fold change.