I want to ask the question regarding the usage of the pre-ranked gene set.
E.g. I have the results of differential expression analysis results obtained with DESeq2 or edgeR. Thus, I have results table with such metrics with LFC, p.adf (or FDR) and etc.
I wonder should I use in fgsea analysis all genes with estimated LFC values (from results table) or is it better to restrict set by p.adj (or FDR) < 0.05 and use only differentially expressed genes?
Thanks for helping!
Best wishes, Alexandr