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Lance Palmer wrote: > I am analyzing some affy data. I have used limma to generate a list of > differentially expressed genes. > > > > > >>From topTable > > > > ID M A t P.Value B > > 36593 227337_at 3.0 9.0 15.3 0.032 -1.5 > > 10619 201170_s_at 2.8 7.3 13.5 0.032 -1.6 > > 19183 209774_x_at 3.1 6.7 13.1 0.032 -1.6 > > 13022 203574_at 1.4 5.9 12.8 0.032 -1.6 > > . > > > > I want to associate gene descriptions to the table. How about (untested): names <- sapply(mget(ids, hgu133plus2GENENAME), function(x) x[1]) ## you could use unlist here, but if there are multiple genenames then ## the length of 'names' would be too long my.table <- data.frame("Names" = names, tt) HTH, Jim > > > > If I do > > tt<- topTable(eb, coef=1, adjust="fdr") > > ids<-tt$ID > > library(hgu133plus2) > > gn<-as.list(hgu133plus2GENENAME) > > top<-gn[ids] > > > > > > top just has a list as follows. > > > > $"227337_at" > > [1] "ankyrin repeat domain 37" > > > > $"201170_s_at" > > [1] "basic helix-loop-helix domain containing, class B, 2" > > > > $"209774_x_at" > > [1] "chemokine (C-X-C motif) ligand 2" > > > > $"203574_at" > > [1] "nuclear factor, interleukin 3 regulated" > > > > > > How do I associate the gene names with the topTable output shown above. > > Better yet, is there a way to include this information anywhere in the > pipeline so that it is included in the topTable. > > (ie before lmFit is utilized) > > > > Thanks, > > > > Lance Palmer > > > > > > PS here is the pipeline I am using > > > > targets<-readTargets("targets.txt") > > data<-ReadAffy(filenames=targets$filename) > > eset<-rma(data) > > exp<-targets$Name > > design<-model.matrix(~-1+factor(exp)) > > colnames(design)<-c("SH","FT") > > contrast.matrix <- makeContrasts(SH-FT, levels=design) > > fit <- lmFit(eset, design) > > fit2 <- contrasts.fit(fit, contrast.matrix) > > eb <- eBayes(fit2) > > topTable(eb, coef=1, adjust="fdr") > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.