[BioC] gene set enrichment

[Gordon K Smyth]

Dear Al,

The obvious answer is the goseq package.  However you have already 
received assistance with goseq:

   https://stat.ethz.ch/pipermail/bioconductor/2012-February/043779.html

So if you are not trying to do a Gene Ontology analysis like goseq does, 
what is it that you are trying to do?

The term "gene set enrichment analysis" was coined by the Broad Institute:

   http://www.broadinstitute.org/gsea/

but you certainly can't simply give a list of genes to GSEA.  It requires 
complete data and is designed for microarrays rather than RNA-Seq anyway.

Best wishes
Gordon

----------------- original message -----------------
[BioC] gene set enrichment
Alpesh Querer alpeshq at gmail.com
Sun Dec 2 01:27:41 CET 2012

Hello all,

I have list of differentially expressed genes from an rna-seq analysis. 
Also, I have a two-column annotation file for the organism with the 
columns being gene and goterm. please guide me towards a bioconductor 
package or any other tool that I could use my list and annotation file as 
input and do gene set enrichment analysis.

Thanks,
Al

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