In a typical DESeq2 output file there are 6 numbers given for each gene; baseMean, log2FoldChange, lfc, stat, pvalue and padj. Each of them have 15 digits. I think this is because R produces 15 digits when it does a calculation. However, these numbers are being derived from measurements and measurements have significant figures and I would not think that that the measurements for gene counts would have 15 significant figures.

Why does this matter to me ? Because, I want to have a cutoff for calling genes accepted as differentially regulated; either a cutoff for padj or log2FoldChange or both and I would like to be consistent and be using the best practice. Say, I choose a cutoff of padj of 0.05. But, the number of genes resulting will depend on how you round off the 15 digit number given for padj. Do you round to two digits after the decimal point, 0.05 (this will include genes with padj of 0.054 or less), or three, 0.050 (this will include genes of 0.0504 or less), or 4, 0.0500, or use the whole 15 digit number with no rounding which, I would think, has too many significant figures.

Also, one more question. If you have a padj cutoff off of 0.05, do you include 0.05 ? Frequently, you hear the cutoff was 0.05, but it usually is not specified if that means less than 0.05 or less than and equal to 0.05.

I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely involved with pure technical edge cases rather than interpreting your sctual analysis results. From what I can say padj < 0.05 is a general agreement. Recommend to use that and focus on interpretation of results rather than postdecimals. If you feel like you have too many DEGs consider testing against a fold change as described in the vignette.