I am trying to perform a GSEA for ten biochemical properties to check which properties are enriched for my set of genes. I am using the Windows application (v4.2.2) with GSEAPreranked package. However, when I perform the analysis some of them returns a p-value of "0.0". When I checked the user guide it states:

"In the GSEA report, a p value of zero (0.0) indicates an actual p value of less than 1/number-of-permutations. For example, if the analysis performed 100 permutations, a reported p value of 0.0 indicates an actual p value of less than 0.01. For a more accurate p value, increase the number of permutations performed by the analysis. Typically, you will want to perform 1000 permutations (phenotype or gene_set). (If you attempt to perform significantly more than 1000 permutations, GSEA may run out of memory.)"

I tried increasing the permutation to 10,000 and 100,000 which still yielded a "0.0" value. Is there a way to calculate the absolute p-value which I can use to later calculate FDR q-value?
You may want to consider switching to [fgsea](http://bioconductor.org/packages/release/bioc/html/fgsea.html) which has algorithmic improvements to GSEA for better p-value estimation [[PREPRINT](https://www.biorxiv.org/content/10.1101/060012v3)]. It helps to resolve most cases where the p-value is really small.