I have been doing some Gene Ontology enrichment analyses for a non model species using the goseq R package. For visualization I would like to use the fold-enrichment of the respective GO-terms. The output columns are a bit confusing to me though:
category = GO -Identifyer numDEInCat = number of genes in the geneset associated with category. nimInCat = total genes associated with the category (what is called universe/back ground in packages like TOPGO)
Total = total number of genes provided in the bias cdna function ClusterSize =?
I would expect to calculate the fold change based on the number of genes for one go-category to be found in the gene set. Like numInCat/total background genes =expected foldchange would then be numDEInCat/expected.
The total number of background genes is not returned though.
Has anyone else calculated GO-fold enrichment from the goseq output before?