Just to add one more little thing to Wolfgangs terrific post, the GOstats package also has some nice vignettes that can get you started using this stuff with GO which is a very common thing people want to do when they are asking these kinds of questions. And it is also possible to do a similar thing using KEGG annotations which might be a good match for your metabolic pathway questions. http://www.bioconductor.org/packages/release/bioc/html/GOstats.html Marc On 08/10/2010 07:32 AM, Wolfgang Huber wrote: > Dawn, > > have a look at the Category, GSEABase, topGO and BioNet packages and > in particular their vignettes. Check also: Bioinformatics. 2008 Nov > 15;24(22):2586-91. Gene set enrichment analysis using linear models > and diagnostics. Oron AP, Jiang Z, Gentleman R. > > Apologies to everyone I did not mention - there is a lot of good > literature (and software) on gene set enrichment analysis out there, > which I will not try to review here, entering "gene set enrichment > analysis" in Pubmed or Google Scholar would be a good start. > > Best wishes > Wolfgang > > > Dawn scripsit 08/08/10 12:50: >> Hi, >> >> I have two groups(one is for control) of genomic data and try to do >> metabolic pathway analysis using Bioconductor. Would you please give >> me some >> suggestion about what packages I should use and the information about >> how I >> can start (e.g., the tutorial )? I hope to see which genes are up and >> down >> in particular pathwa*y such as the insulin pathway.* >> * >> * >> *Thank you very much!* >> *Dawn* >> >> [[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 > >

I also like the package 'pcot2' written by Sarah Song. It checks all KEGG pathways by default but you can, with a little elbow grease, define your own genesets to test as well. I like it better the GSEA etc because it is a true multivariate test (Hotellings T-square) Martha Sent from my Verizon Wireless BlackBerry -----Original Message----- From: Wolfgang Huber <whuber@embl.de> Sender: bioconductor-bounces at stat.math.ethz.ch Date: Tue, 10 Aug 2010 16:32:18 To: <bioconductor at="" stat.math.ethz.ch=""> Subject: Re: [BioC] package for pathway analysis Dawn, have a look at the Category, GSEABase, topGO and BioNet packages and in particular their vignettes. Check also: Bioinformatics. 2008 Nov 15;24(22):2586-91. Gene set enrichment analysis using linear models and diagnostics. Oron AP, Jiang Z, Gentleman R. Apologies to everyone I did not mention - there is a lot of good literature (and software) on gene set enrichment analysis out there, which I will not try to review here, entering "gene set enrichment analysis" in Pubmed or Google Scholar would be a good start. Best wishes Wolfgang Dawn scripsit 08/08/10 12:50: > Hi, > > I have two groups(one is for control) of genomic data and try to do > metabolic pathway analysis using Bioconductor. Would you please give me some > suggestion about what packages I should use and the information about how I > can start (e.g., the tutorial )? I hope to see which genes are up and down > in particular pathwa*y such as the insulin pathway.* > * > * > *Thank you very much!* > *Dawn* > > [[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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber _______________________________________________ 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