I am trying to perform a GSEA preranked analysis from a paired RNAseq analysis, and I have 2 questions:
When the DESeq2 analysis is performed, a lot of genes include NAs values inside the dataframe, in the columns of Log2FC, padj, etc. To perform the GSEA, we have to use ALL the genes, and I think that is obvious that I have to eliminate the NAs values from Log2FC (if it is the value of ranking the list), but what happen with the NAs values in padj genes?? They have their own Log2FC value (altough the padj is NAs). Should I remove them? Or put them all in the analysis?
Which value of the DESeq2 results should I use to prerank the genes? The Log2FC? The stat?
Thanks a lot!! :D