Hi everyone, just a quick question

I am about to generate my volcano plots for DEG analysis after DESeq2.

I am wondering if I should use my normal DESeq2 results, or the results I have applied LFC Shrinkage too?

What is the reasoning behind this choice?

And finally, should I do the same thing when counting the number of DEGs between conditions in a Venn diagram?

Thank you in advance!

This is really up to you. See the apeglm paper for discussion of the MLE (what comes out of results) vs posterior effect sizes (from lfcShrink).

For counting DEG, most users consider the padj from either a point null or a banded null hypothesis.