Hi, Can anyone help me by providing hints in writing a function that takes a list of entrez gene identifiers as an input(e.g. differentially expressed genes in a gene expression study) and a list of background genes (e.g. entrez gene identifiers of all probed genes on the microarray) and performs a hypergeometric test for over representation against GO and KEGG. Regards, Pradee.

On 11/02/2010 09:22 AM, Pradeep Battula wrote: > Hi, > > Can anyone help me by providing hints in writing a function that takes a list of entrez gene identifiers as an input(e.g. differentially expressed genes in a gene expression study) and a list of background genes (e.g. entrez gene identifiers of all probed genes on the microarray) and performs a hypergeometric test for over representation against GO and KEGG. > Hi Pradee -- have you looked at the BiocViews http://bioconductor.org/help/bioc-views/release/BiocViews.html 'Software' 'Annotation' packages? Martin > Regards, > Pradee. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

On Tue, Nov 2, 2010 at 12:22 PM, Pradeep Battula <prabat@utu.fi> wrote: > Hi, > > Can anyone help me by providing hints in writing a function that takes a > list of entrez gene identifiers as an input(e.g. differentially expressed > genes in a gene expression study) and a list of background genes (e.g. > entrez gene identifiers of all probed genes on the microarray) and performs > a hypergeometric test for over representation against GO and KEGG. > Hi, Pradeep. Have a look at the topGO package, for example. There are several other packages that are highly relevant. Sean [[alternative HTML version deleted]]