Hi I have a set of differentially expressed genes from a microarray experiment. I want to to do enrichment analysis based on chromosomes. Please suggest a package or another strategy. Gaurav Bhatti [[alternative HTML version deleted]]

On 07/27/2010 06:56 AM, Bhatti, Gaurav wrote: > Hi > > I have a set of differentially expressed genes from a microarray > experiment. I want to to do enrichment analysis based on chromosomes. > Please suggest a package or another strategy. Hi Gaurav -- the 'Category' package has a vignette describing this, and the subtleties involved. http://140.107.3.23/packages/release/bioc/html/Category.html Also the references in the vignette and http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/22/25 86 Martin > > Gaurav Bhatti > > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Gaurav, You may try GSEA, I think. Steve On Tue, Jul 27, 2010 at 9:56 AM, Bhatti, Gaurav <gbhatti@med.wayne.edu>wrote: > Hi > > I have a set of differentially expressed genes from a microarray > experiment. I want to to do enrichment analysis based on chromosomes. Please > suggest a package or another strategy. > > Gaurav Bhatti > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]