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                                            ajw2329

collapsePathways() errors in padj threshold-dependent fashion after successful fgsea() run

Thanks for your reply. I've attached the ranked genes (as a two column TSV with gene in col 1 and score in col 2 ordered by score descending) as well...

collapsePathways() errors in padj threshold-dependent fashion after successful fgsea() run

Thanks very much! I'm guessing the reason that lowering the padj threshold to 0.01 worked was because pathways that included genes with NA rank were coincidentally removed ?