Hello, I am aware of two tools that allow to test gene enrichment on an ordered list of genes (rather than comparing a set of differentially regulated genes with a background list): GOrilla ( http://cbl-gorilla.cs.technion.ac.il/) and GOstat ( http://gostat.wehi.edu.au/). Both seem to work pretty well for my purposes, but both are only implemented as services available through a web interface. Is there already any package like this available for R / Bioconductor? Kind regards, January -- -------- January Weiner -------------------------------------- [[alternative HTML version deleted]]

Hi January, On Mon, Apr 22, 2013 at 3:59 AM, January Weiner <january.weiner at="" gmail.com=""> wrote: > Hello, > > I am aware of two tools that allow to test gene enrichment on an ordered > list of genes (rather than comparing a set of differentially regulated > genes with a background list): GOrilla ( > http://cbl-gorilla.cs.technion.ac.il/) and GOstat ( > http://gostat.wehi.edu.au/). Both seem to work pretty well for my purposes, > but both are only implemented as services available through a web interface. > > Is there already any package like this available for R / Bioconductor? Would GSEA (and similar tests) do the trick for you? You'll find a few packages in bioc-land to run GSEA-like tests for you by searching for GSEA in the bioc software page. Hidden in limma is `romer` which also does similar testing using linear models. Coincidentally, the author of the new `piano` package posted an announcement of it being publicly available for use on the bioc-devel list soon after you posted your question, which you might have missed -- I haven't used it, but the announcement suggests that it does GSEA as well, so perhaps another option. HTH, -steve -- Steve Lianoglou Computational Biologist Department of Bioinformatics and Computational Biology Genentech

On 04/22/2013 03:59 AM, January Weiner wrote: > Hello, > > I am aware of two tools that allow to test gene enrichment on an ordered > list of genes (rather than comparing a set of differentially regulated > genes with a background list): GOrilla ( > http://cbl-gorilla.cs.technion.ac.il/) and GOstat ( > http://gostat.wehi.edu.au/). Both seem to work pretty well for my purposes, > but both are only implemented as services available through a web interface. > > Is there already any package like this available for R / Bioconductor? The Category package http://bioconductor.org/packages/release/bioc/html/Category.html vignette "Using Categories to Analyze Microarray Data" walks through one approach; I don't know if this qualifies as 'ordered' for your purposes. Martin > > Kind regards, > > January > -- 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