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Hi Burak -- GSEABase is meant to provide infrastructure for gene-set based operations, rather than implementations of gene set enrichment algorithms. The PGSEA package might be a useful direction to explore (with or without GSEABase -- you could use getBroadSets to retrieve predefined gene sets, feed GeneSetCollections into the PGSEA function, or use GeneSet objects to subset an ExpressionSet, for instance). There are differing opinions about what constitutes gene set enrichment analysis; for one view see the slides from the recent Bioconductor workshop in Chicago, e.g., GSEA07.pdf or Category.R; available from http://daisy.prevmed.northwestern.edu/~denise/BiocChicago2007/ or by navigating from bioconductor.org -> workshops tab. Hope that helps, Martin burak kutlu <burak_kutlu at="" yahoo.com=""> writes: > I am looking at the GSEABase vignette on how to create GeneSets. > I was wondering if there is an example of how to use these sets to perform the actual GSEA analysis. > Thanks in advance > -burak > > > > __________________________________________________ > > > > [[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