"N/A" in fgsea result

Question

[puffpumpkin]

Hi! I am using this code to run gsea: fgsea( pathways = hallmark, stats = fc_vec, scoreType = 'std', minSize = 15, maxSize = 500, nPermSimple = 1000000)

Some of the pathways return "N/A" for p values, enrichment scores, etc., other pathways gave me a number for . Why is this the case? I do notice that increasing nPermSimple helps sometimes (i.e. the N/A became numbers). What should I do to fix this problem?

thank you!

[Dave Carlson]

Did you get any warnings in the fgsea output? Per the following, there should be some info in the warnings pointing you in the direction of what the problem may be.

https://github.com/ctlab/fgsea/issues/97