What does gene ratio and count mean as output of the gseGO function?
Entering edit mode
13 months ago
Wocher33 ▴ 10

Hi all,

I got log FoldChanges for my RNAseq dataset and put them in decreasing order with the ensembl ID into the gseGO() function. The results make sense from an biological perspective but I have a bit of a problem interpreting the results.

dotplot() shows besides adjusted p-value the stats "count" and "gene ratio". I know that this question has been asked before here and has received an answer, but could someone explain again what the meaning of "count" and "gene ratio" in case of gseGO() is?

I think I understand that the gene ratio is the overlap of differentially expressed genes with genes from a specific gene set, divided by the overlap of differentially expressed genes with all gene sets. But what sense does it make for gseGO() where I put in all genes with their log Fold change.

Thanks for your help!

clusterProfiler RNAseq • 413 views

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