Im using clusterProfile clusterProfiler_3.0.5 on R 3.3.1 as follows :
kegg <- enrichKEGG(entrez_id, organism="hsa", pvalueCutoff=0.05, pAdjustMethod="BH", qvalueCutoff=0.2,use_internal_data=FALSE) write.csv(summary(kegg),file=paste0(c(getwd(),dir_pathway,"DESEQ_KEGG_ENRICHMENT.csv"),collapse="/"))
I have two questions:
I don't understand how works the pvalue and qvalue. pvalueCutof is just use for filtering on pAdjusted value or raw p-value ?
In my output, I have lines with a qvalue upper to 0.2 whereas my qvalueCutoff is set to 0.2. Is this a bug or qvalueCutoff is used for another thing than simply filtering here.
What is q-value ? I set to 0.2 (taken from an example) But is it a kind of FDR...? Kind of relative to that conceptual question about FDR, FDR adjusted p-value and q-value