Question on number of genes used in GO analysis
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Danté • 0
@13ba9fa8
Last seen 7 weeks ago
United States

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.

GO clusterProfiler • 292 views
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@james-w-macdonald-5106
Last seen 20 hours ago
United States

Not all NCBI IDs have a GO BP term associated.

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Thanks, that makes a lot of sense!

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