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Hi Tarun, Tarun Nayar wrote: > Hi, > > I've output a 'gt.result' in a globaltest analysis of a microarray > experiment. This is a class with a number of slots summarizing the > results of a globaltest on a number of genesets. In this experiment I > tested the association of a number of GO IDs with gene expression. I'd > like to convert these IDs to GO Terms for ease of interpretation. > > Genes Tested Statistic Q Expected Q sd of Q P-value > FDR.adjusted > GO:0008318 5 5 36.929 5.6901 5.0507 0.0010123 > 0.70613 > GO:0018344 3 3 53.234 5.2187 7.0999 0.0011494 > 0.70613 > GO:0018348 3 3 53.234 5.2187 7.0999 0.0011494 > 0.70613 > > The method to convert KEGG Pathway IDs to KEGG Pathway Names is as > follows (for a 'gt.result' called "top20_k") > > >>names(top20_k) <- as.list(KEGGPATHID2NAME)[names(top20_k)] > > > Is there a similar command to convert GO IDs in this context? > library(GO) > library(annotate) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. > gos <- ls(GOTERM)[5:15] > gos [1] "GO:0000006" "GO:0000007" "GO:0000009" "GO:0000010" "GO:0000011" [6] "GO:0000012" "GO:0000014" "GO:0000015" "GO:0000016" "GO:0000017" [11] "GO:0000018" > sapply(mget(gos, GOTERM), Term) GO:0000006 "high affinity zinc uptake transporter activity" GO:0000007 "low-affinity zinc ion transporter activity" GO:0000009 "alpha-1,6-mannosyltransferase activity" GO:0000010 "trans-hexaprenyltranstransferase activity" GO:0000011 "vacuole inheritance" GO:0000012 "single strand break repair" GO:0000014 "single-stranded DNA specific endodeoxyribonuclease activity" GO:0000015 "phosphopyruvate hydratase complex" GO:0000016 "lactase activity" GO:0000017 "alpha-glucoside transport" GO:0000018 "regulation of DNA recombination" Best, Jim > > Thanks > > Tarun Nayar > Genome Sciences Centre > Vancouver, BC > > [[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 -- 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.

>Is there a similar command to convert GO IDs in this context? Would this work for you? >library(GO) >library(Biobase) >goTerms <- lapply(mget(c("GO:0051937", "GO:0051938", "GO:0051939"), GOTERM), FUN = function(x) Term(x)) > >Thanks > >Tarun Nayar >Genome Sciences Centre >Vancouver, BC > > [[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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084