I wonder why, in the results of enrichGO(), the total number of genes mentionned in GeneRatio is different from the number of genes in my input?
In one analysis, I have 858 ENTREZID genes in input. After running enrichGO()
GOenrichment_BP = enrichGO(gene_id$ENTREZID, OrgDb=org.Hs.eg.db, keytype = "ENTREZID", ont = "BP", pvalueCutoff = 0.001, pAdjustMethod = "BH", qvalueCutoff = 0.001, minGSSize = 5, maxGSSize = 900, readable = TRUE)
I get the first 2 lines:
ID Description GeneRatio BgRatio GO:0070482 response to oxygen levels 46/740 301/16672 GO:0036293 response to decreased oxygen levels 44/740 285/16672
Why are there now 740 genes?
Maybe I am missing something obvious here. It would be nice to have some explanation.