No Go Terms For Genes When Using The Gostat Package In Bioconductor

Question

[shaikhfarahdeeba]

Hi can anybody plz help me regarding differential gene expression analysis i m using a dataset of affymetrix hgu133plus2 and carried out analysis using limma in r and other bioconductor package but when i tried doing gene set enrichment analysis using GOstats i am getting an error like

Error in getGoToEntrezMap_db(p) : 
    The genes you are testing do not have any corresponding GO terms for the ontology you are searching

Kindly give a solution.

Answer 1

[Charles Warden]

If you have a table of gene symbols from limma, I would just use one of the many web-based GO enrichment tools.

GATHER is probably my favorite: (and you can then easily do other types of functional enrichment)

http://gather.genome.duke.edu/