clusterProfiler - difference in the number of genes from input and enrichGO results
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@jane-merlevede-5019
Last seen 3.3 years ago

Hello,

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.

Thank you

clusterProfiler • 1.5k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 11 months ago
China/Guangzhou/Southern Medical Univer…

Two cases:

1. If your input gene id contains duplicated IDs, those duplicated will be removed.

2. Those genes that do not have GO annotation will be removed.

 

 

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In the case of this analysis, I have no duplicated ID. So 14% of my ENTREZID genes do not have a GO annotation.

Is it a classic percentage? What do you get usually?

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