Dear Group, does limma provide gene set enrichment through a wilcoxon rank sum test? I overheard someone discussing that enrichment scores provided through this method (limma - wilcoxon rank sum) are better than GSEA enrichment scores. I see some old 2005 tutorials usings Dr. Smiths gene set test. I am finding difficult to find any vignette that discuss Gene set test and wilcoxon rank sum. Are there any new changes to limma towards advanced gene set test version. Please suggest. thanks srini

Yes, limma does. ?geneSetTest tells you about it. Written by Dr Smyth, not Dr Smith. M. On 30/11/2007, at 12:11 PM, Srinivas Iyyer wrote: > Dear Group, > > > does limma provide gene set enrichment through a > wilcoxon rank sum test? > > I overheard someone discussing that enrichment scores > provided through this method (limma - wilcoxon rank > sum) are better than GSEA enrichment scores. > > I see some old 2005 tutorials usings Dr. Smiths gene > set test. > > I am finding difficult to find any vignette that > discuss Gene set test and wilcoxon rank sum. > Are there any new changes to limma towards advanced > gene set test version. > > Please suggest. > thanks > srini > > _______________________________________________ > 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

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