[BioC] Can I know the number of genes in enriched GO category using GOseq

Biase, Fernando biase at illinois.edu
Fri Mar 4 18:31:45 CET 2011


Hi everyone,

I am running differential gene (DE) expression analysis using RNA-seq data  and I have used GOseq to find enriched Gene Ontology (GO) categories in the DE genes list.
I have a couple of questions to ask, and hope someone can help me:

Can I extract the number of genes, and IDs present in each enriched category using GOseq?

If not, I suppose it is better to annotate all the genes for GO and find out which genes are annotated in a particular category. Is there a R-package that you would recommend to annotate  genes using ENSEMBL and NCBI gene_IDs?

Thanks,
Fernando



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