I am doing RNAseq analysis for DEG using Deseq2 package. I am trying to subset my list of DEG using both padj value and log2FC.
I have analysed my results using the Deseq() function and extracted the results using results().
I have also shrunken my Log2FC using lfcShrink().
My question is simply, when I am subseting my list of DEG, should I used the padj values from results() or lfcShrink(), as they are different. (I will be using the log2FC results from lfcShrink). I have read that performing the lfcShrink() function shouldnt change the list of DEG but obviously the list will change if I use the padj from lfcShrink().
Is the padj from lfcShrink a more reliable value or is it just a more conservative method? Thank you.