Hi! I have rna-seq data for samples that were exposed to environmental stressors across two timepoints in a fully factorial design (so, let's say my sample treatments are CC, CS, SC, and SS, where c is control, s is a stressor, and the first letter is the treatment of the first exposure and the second letter is the treatment of the second exposure). I have used DESeq2 to identify differentially expressed genes within pairwise comparisons. Based on the DESeq manual and other threads, I've applied a lfc shrinkage estimator to be able to compare my LFCs across pairwise comparisons - is that correct? or should I be using the raw LFC values?

Thank you!

Try the vignette which has a lot of information on these type of questions.