Hello! I'm new to bioconductor and am trying to use the simpleaffy package. My example is simple: >library(simpleaffy) >library(ygs98cdf) > x <-read.affy() > x.rma<-call.exprs(x,"rma") Background correcting Normalizing Calculating Expression pw<-pairwise.comparison > pw<-pairwise.comparison(x.rma,"treatment",c("n","a")) > pw.filtered<-pairwise.filter(pw) > summary<-results.summary(pw.filtered,'ygs98cdf') Error in get(x, envir, mode, inherits) : variable "ygs98cdfSYMBOL" was not found Any ideas? Apologies if this is the wrong list for this mail. cheers, shawn

There is no annotation for SYMBOL in any of the annotation packages for yeast because there were no source data available for SYMBOL when the packages were built. >X-Original-To: jzhang@jimmy.harvard.edu >Delivered-To: jzhang@jimmy.harvard.edu >Date: Wed, 23 Mar 2005 02:13:09 -0800 >From: Shawn Hoon <shawnh@stanford.edu> >User-Agent: Mozilla Thunderbird 1.0 (Macintosh/20041206) >X-Accept-Language: en-us, en >MIME-Version: 1.0 >To: bioconductor@stat.math.ethz.ch >Content-Transfer-Encoding: 7bit >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch does not designate permitted sender hosts) >Received-SPF: none (hypatia: domain of shawnh@stanford.edu does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >X-Mailman-Approved-At: Thu, 24 Mar 2005 15:39:01 +0100 >Subject: [BioC] variable "ygs98cdfSYMBOL" was not found >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.5 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu >X-Spam-Level: >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham version=3.0.1 > >Hello! > > I'm new to bioconductor and am trying to use the simpleaffy package. >My example is simple: > > >library(simpleaffy) > >library(ygs98cdf) > > x <-read.affy() > > x.rma<-call.exprs(x,"rma") >Background correcting >Normalizing >Calculating Expression >pw<-pairwise.comparison > > pw<-pairwise.comparison(x.rma,"treatment",c("n","a")) > > pw.filtered<-pairwise.filter(pw) > > summary<-results.summary(pw.filtered,'ygs98cdf') >Error in get(x, envir, mode, inherits) : variable "ygs98cdfSYMBOL" was >not found > >Any ideas? > >Apologies if this is the wrong list for this mail. > >cheers, > >shawn > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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

It's been several years since I worked with yeast data, but I do recall a file called something like alias.txt from a stanford site which had lists of all the symbols for yeast genes. Many genes had many different symbols associated with it, so it wasn't much fun. Perhaps someone can comment on whether or not a set of unique yeast gene symbols has since then been agreed upon, i.e. to allow 1-to-1 mappings between gene symbols and ORFs. Tom ----- Original Message ----- From: "John Zhang" <jzhang@jimmy.harvard.edu> To: <shawnh@stanford.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Thursday, March 24, 2005 9:47 AM Subject: Re: [BioC] variable "ygs98cdfSYMBOL" was not found > There is no annotation for SYMBOL in any of the annotation packages for > yeast > because there were no source data available for SYMBOL when the packages > were > built. > > >>X-Original-To: jzhang@jimmy.harvard.edu >>Delivered-To: jzhang@jimmy.harvard.edu >>Date: Wed, 23 Mar 2005 02:13:09 -0800 >>From: Shawn Hoon <shawnh@stanford.edu> >>User-Agent: Mozilla Thunderbird 1.0 (Macintosh/20041206) >>X-Accept-Language: en-us, en >>MIME-Version: 1.0 >>To: bioconductor@stat.math.ethz.ch >>Content-Transfer-Encoding: 7bit >>Received-SPF: none (hypatia: domain of >>bioconductor-bounces@stat.math.ethz.ch > does not designate permitted sender hosts) >>Received-SPF: none (hypatia: domain of shawnh@stanford.edu does not >>designate > permitted sender hosts) >>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >>X-Mailman-Approved-At: Thu, 24 Mar 2005 15:39:01 +0100 >>Subject: [BioC] variable "ygs98cdfSYMBOL" was not found >>X-BeenThere: bioconductor@stat.math.ethz.ch >>X-Mailman-Version: 2.1.5 >>List-Id: The Bioconductor Project Mailing List >><bioconductor.stat.math.ethz.ch> >>List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >>List-Post: <mailto:bioconductor@stat.math.ethz.ch> >>List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, > <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on > pascal.dfci.harvard.edu >>X-Spam-Level: >>X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00 autolearn=ham > version=3.0.1 >> >>Hello! >> >> I'm new to bioconductor and am trying to use the simpleaffy package. >>My example is simple: >> >> >library(simpleaffy) >> >library(ygs98cdf) >> > x <-read.affy() >> > x.rma<-call.exprs(x,"rma") >>Background correcting >>Normalizing >>Calculating Expression >>pw<-pairwise.comparison >> > pw<-pairwise.comparison(x.rma,"treatment",c("n","a")) >> > pw.filtered<-pairwise.filter(pw) >> > summary<-results.summary(pw.filtered,'ygs98cdf') >>Error in get(x, envir, mode, inherits) : variable "ygs98cdfSYMBOL" was >>not found >> >>Any ideas? >> >>Apologies if this is the wrong list for this mail. >> >>cheers, >> >>shawn >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >