Hi,

Does anyone know if you should remove the genes that fail independent filtering in deseq2 (I.e have NA padj values). I've read discussion around its purpose for deseq2 but I'm not sure how these genes should be treated when performing GSEA. 

Removal of these genes before running fGSEA tends to result in finding more pathways (and higher padj values) which aligns with the idea of having higher power. However I want to make sure using this approach is valid. 

Thank you. 
Yes. Independent filtering is a methodology to improve F1 score by removing genes with low variance, mean expression, dispersion, or other noise surrogate. Genes that are removed by IF should be regarded as "not effectively profiled" and ignored in downstream analysis. 