Sorry but it doesn't work: > get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep= ""),KEGGPATHID2EXTID) Error in get(x, envir, mode, inherits) : variable "Biosynthesis of steriods" not find -----Messaggio originale----- Da: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] Per conto di John Zhang Inviato: gioved? 16 giugno 2005 16.55 A: michael.auer at meduniwien.ac.at; rhaddad at genetics.wayne.edu Cc: bioconductor at stat.math.ethz.ch Oggetto: Re: [BioC] Pathway Information Suppose you are looking for gene that are involved in human "Biosynthesis of steriods" pathway, the following will give you a vector of Entrez Gene ids: >library(KEGG) >get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep = ""), KEGGPATHID2EXTID) >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >From: Ramsi Haddad <rhaddad at="" genetics.wayne.edu=""> >To: michael.auer at meduniwien.ac.at >Mime-Version: 1.0 >Date: 16 Jun 2005 09:58:13 -0400 >Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is authenticated by a trusted mechanism) >Received-SPF: none (hypatia: domain of rhaddad at genetics.wayne.edu does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Cc: bioconductor mailing list <bioconductor at="" stat.math.ethz.ch=""> >Subject: Re: [BioC] Pathway Information >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.6 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >Content-Transfer-Encoding: 7bit >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu >X-Spam-Level: >X-Spam-Status: No, score=-2.2 required=3.0 tests=AWL,BAYES_00 autolearn=ham version=3.0.1 > > >Dear Michael, > There is a pretty good description in the globaltest vignette. Most of >the stuff shown below is based on it: > >library(mgu74av2) >library(KEGG) > >### this next line generates a list of kegg pathways and all >### the probe sets that belong in a given pathway. >mouse.kegg.sets <- as.list(mgu74av2PATH2PROBE) > >### the next 3 lines give the names of the pathways from their >### kegg ID numbers >all.kegg.ids <- ls(KEGGPATHID2NAME) >all.kegg.names <- mget(all.kegg.ids, KEGGPATHID2NAME) >table.of.keggs <- as.matrix(unlist(all.kegg.names)) >write.table(table.of.keggs, "keggs.csv", sep=",",col.names=NA, >row.names=T) > >### here's how to get the name of a given kegg pathway: >what.is.00010 <- get("00010", KEGGPATHID2NAME) ## this is glycolysis. > >### here's how to get the probesets in the Glycolysis Path from the >mouse array: >glycolysis.affyIDs <- get("00010", mgu74av2PATH2PROBE) ## there are 68 >such probe sets. >another.glycolysis.affyIDs <- mouse.kegg.sets[["00010"]] ## more than >one way to skin a cat > >### here's how to get the kegg pathway numbers for anything with >"Cholera" >colera.kegg.paths.index <- grep("Cholera", table.of.keggs) ## this >provides the index >colera.keggs <- table.of.keggs[colera.kegg.paths] >### here it is in one step: >### table.of.keggs[grep("Cholera", table.of.keggs)] > >hope that gets you started. > >Ramsi > > > > >> Hi >> >> Can anybody tell me the following >> >> I want to identify genes which are located on a certain pathway NF Kappa. >> How can I obtain such an information. Which package is appropriate and >> which commands are needed. If any body ever encounterd the same problem >> please let me know. >> >> Michael >-- >Ramsi Haddad, Ph.D. >Center for Molecular Medicine and Genetics. >Functional Genomics Laboratory, >Perinatology Research Branch, NICHD, NIH. >259 Mack Avenue, >Room 3146 Applebaum Bldg. >Detroit, MI 48201, USA. > >phone:(313) 577-2569 / fax:(313) 577-7736 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Well, if so (regarding R and BioC in the back end, or other open source projects), it is considered collegial to state that on the front end and acknowledge the hard work of all the developers whose programs you are using. And please do read the posting guide, as this has nothing to do with the subject line. Best wishes, Robert David Kipling wrote: > Hi > > Apologies to all for this being not strictly speaking BioC (although the back > end does use some R/BioC functions to make heatmaps and the like)! > > Have a look at: > > http://www.madras.uwcm.ac.uk/ > > This is an Affy-focussed web-based environment where you can upload and review > your data in a gene-centric fashion whilst also getting a biologist- friendly > "executive summary" of what that gene does. It's free :-) > > There is a public guest login option which gives you a few token public datasets > to browse. If you go into Pathways you'll find we've dumped all the BioCarta > pathways into it as well, including NFkappa B. Select this and you get all the > genes on your affy chip from this pathway and browse away. > > If anyone wants to discuss this with me in more detail (e.g. how to get a login > or local install) then please contact me off-list. > > Regards > > David > > > Professor David Kipling > Department of Pathology, > School of Medicine, > Cardiff University, > Heath Park > Cardiff CF14 4XN > > Email: KiplingD at cardiff.ac.uk > Tel: +44 29 2074 4847 > fax: +44 29 2074 4276 > >>>>"Auer Michael" <michael.auer at="" meduniwien.ac.at=""> 06/16/05 10:24 AM >>> > > Hi > > Can anybody tell me the following > > I want to identify genes which are located on a certain pathway NF Kappa. > How can I obtain such an information. Which package is appropriate and > which commands are needed. If any body ever encounterd the same problem > please let me know. > > Michael > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >