I have recently noticed a small discrepancy in the number of genes when running EnrichGO: the resulting GeneRatio column has 65 as the denominator (eg. 3/65, 12/65, 7/65...), however, in the dataframe i fed into the enrichGO() function there was clearly 71 rows (genes)

heres my code:

enrichGO(gene = df$ENTREZID, 
                   OrgDb = org.Hs.eg.db, 
                   ont = "BP",
                   pAdjustMethod = "BH",
                   pvalueCutoff = 0.05,
                   readable = TRUE)

**this df right here already has the genes which doesn't have an ENTREZID removed.

Please let me know if there is an explanation, any help is greatly appreciated.

Not all NCBI IDs have a GO BP term associated.