Query about gene ontology analysis in edgeR vs GSEA
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2.1 years ago
elizabethR ▴ 70

Hi

I cannot find any similar posts to this on the forum, so please may I ask if anyone can help me?

I have run differential expression on edgeR. I noted that edgeR has a gene ontology and KEGG pathway analysis function so I used it with the code from the users guide and vignette. I downloaded the results into a text file and scrutinised it. It gave me the GO terms that the genes were mapped to, with the process (BP/CC/MF), the number of genes mapped, number of genes from that GO term that are up and number that are down regulated, and then p values for upregulation and downregulation respectively. There are no enrichment scores or normalised enrichment scores, so I figured this analysis is different to the GSEA analysis. However I am not sure what sort of analysis is undertaken in the GO analysis module, and I cannot find any clear info on this in papers/user manual/on the biostars boards or in the programme help. Can anyone advise me what sort of analysis this is and how it is done? Is it purely testing what proportion of the genes assigned to that GO term are up- and down-regulated?

edgeR GO • 868 views
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2.1 years ago
Gordon Smyth ★ 2.5k

Yes, the goana and kegga functions test whether a high proportion of the genes for that GO term (or KEGG pathway) are DE.

See ?goana.

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2.1 years ago
elizabethR ▴ 70

thank you Gordon that is much appreciated