Thank you Our question I think will be rather "simple" We have porcine Affy GeneChip data from Duroc/Yorkshire deep/shallow wounds over time and will just ask if any gene sets are enriched in this data Will probably give them all a try unless you suggest one is clearly "better" Thank you > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Date: Sun, 23 Nov 2008 12:10:32 -0800 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] GSEA > > Loren Engrav <engrav at="" u.washington.edu=""> writes: > >> Greetings >> >> There is the GSEABase in Bioconductor > > GSEABase provides infrastructure for managing sets of genes, and for > mapping between identifiers; it doesn't 'do' a gene set enrichment > analysis. Also, the GSEABase infrastructure came after other R-based > GSEA-like packages and so it may be a bit less useful for what it's > named after than its name suggests. > > GSEA-like analyses in R include PGSEA, Category, GSEAlm, and probably > others. The reasons to choose between these and non-R tools is likely > to be driven by suitability of analysis for question at hand. > > Martin > >> But there is also the GSEA located at www.broad.mit.edu/gsea/ >> >> For a newbie to GSEA, is there any reason(s) to begin with one or the other? >> >> Thank you >> >> -- >> Loren Engrav, MD >> Univ Washington >> Seattle >> >> _______________________________________________ >> 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 M2 B169 > Phone: (206) 667-2793