I'm trying to generate a ranking file for my differential expressed genes that was generated via DESeq2. I saw some websites like Genome Spot that taught me how to use the p-values and log2foldchange to rank the genes. But in DESeq2 output, some of them appear as "NA". And this will reappear in the ranking file. Apparently, pre-ranked GSEA either java Desktop application (from Broad Institute) or GenePattern are not able to process the NA entries.
As such, what should I do for genes that display NA? As in what is the usual procedure in handling such information? Remove them?