Hi, I wish to get the UniGene annotation of the top ranked genes for two sets of Affymetrix files (Diseased vs. Reference; chip type: hgu133a). I am uncertain as to how to approach it. A few of the simple background codes are: dataset <- ReadAffy() ; myRMA <- justRMA() fit <- lmFit (myRMA, design) # Analysis design is in object, “design” contrasts_matrix <- makeContrasts(Diseased-Healthy, levels = design) fit2 <- contrasts.fit (fit, contrasts_matrix) fit3 <- eBayes (fit2) test_results <- topTable(fit3, number=10, adjust="BH") # Then, I was uncertain regarding how to get the output with UniGene ID. Wonder if a bit of tweaking in the function, probes2table should somehow solve this ! # probes2table(****, featureNames(***), "hgu133a.db", anncols = aaf.handler()[c(1,2,7,9)], html = FALSE, text = TRUE, filename = "****") Many thanks, Chintanu > sessionInfo () R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils methods base other attached packages: [1] annaffy_1.16.0 hgu133a.db_2.2.12 affycoretools_1.16.3 KEGG.db_2.2.11 GO.db_2.2.11 RSQLite_0.7-2 DBI_0.2-4 [8] AnnotationDbi_1.6.1 limma_2.18.3 hgu133acdf_2.4.0 affy_1.22.1 Biobase_2.4.1 survival_2.35-7 loaded via a namespace (and not attached): [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 Category_2.10.1 gcrma_2.16.0 genefilter_1.24.2 GOstats_2.10.0 [8] graph_1.22.2 GSEABase_1.6.1 preprocessCore_1.6.0 RBGL_1.20.0 RCurl_1.2-0 tools_2.9.2 XML_2.6-0 [15] xtable_1.5-5 [[alternative HTML version deleted]]

Hi Chintanu, Chintanu wrote: > Hi, > > I wish to get the UniGene annotation of the top ranked genes for two sets of > Affymetrix files (Diseased vs. Reference; chip type: hgu133a). I am > uncertain as to how to approach it. > > A few of the simple background codes are: > > dataset <- ReadAffy() ; myRMA <- justRMA() > > fit <- lmFit (myRMA, design) # Analysis design is in object, ?design? > > contrasts_matrix <- makeContrasts(Diseased-Healthy, levels = design) > > fit2 <- contrasts.fit (fit, contrasts_matrix) > > fit3 <- eBayes (fit2) > > test_results <- topTable(fit3, number=10, adjust="BH") > > # Then, I was uncertain regarding how to get the output with UniGene ID. > Wonder if a bit of tweaking in the function, probes2table should somehow > solve this ! > > # probes2table(****, featureNames(***), "hgu133a.db", anncols = > aaf.handler()[c(1,2,7,9)], html = FALSE, text = TRUE, filename = "****") Did you try it? This should output probe, symbol, gene name and UniGene ID, without any 'tweaking' required. Best, Jim > > Many thanks, > > Chintanu > > > >> sessionInfo () > > R version 2.9.2 (2009-08-24) > > i386-pc-mingw32 > > locale: > > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > > [1] grDevices datasets splines graphics stats tcltk utils > methods base > > other attached packages: > > [1] annaffy_1.16.0 hgu133a.db_2.2.12 affycoretools_1.16.3 > KEGG.db_2.2.11 GO.db_2.2.11 RSQLite_0.7-2 > DBI_0.2-4 > > > [8] AnnotationDbi_1.6.1 limma_2.18.3 hgu133acdf_2.4.0 > affy_1.22.1 Biobase_2.4.1 survival_2.35-7 > > loaded via a namespace (and not attached): > > [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 > Category_2.10.1 gcrma_2.16.0 genefilter_1.24.2 > GOstats_2.10.0 > > [8] graph_1.22.2 GSEABase_1.6.1 preprocessCore_1.6.0 > RBGL_1.20.0 RCurl_1.2-0 tools_2.9.2 > XML_2.6-0 > > > [15] xtable_1.5-5 > > [[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, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826

Hi Chintanu, why don't you try it with biomaRt using the following code: library(biomaRt) # connect to biomaRt server hs.ensembl <- useDataset("hsapiens_gene_ensembl",useMart("ensembl")) # retrieve ID information my.id.list <- getBM(attributes=c("unigene","affy_hg_u133a"),filters="affy_hg_u133a", values=test_results[,1],mart=hs.ensembl) # remove empty unigene IDs my.sub.list <- subset(my.id.list,unigene!="") # attach unigene IDs index <- match(test_results[,1],my.sub.list$affy_hg_u133a) annotated.test_results <- cbind(test_results,my.sub.list$unigene[index]) I hope that helps... Cheers, CJ Chintanu schrieb: > Hi, > > I wish to get the UniGene annotation of the top ranked genes for two sets of > Affymetrix files (Diseased vs. Reference; chip type: hgu133a). I am > uncertain as to how to approach it. > > A few of the simple background codes are: > > dataset <- ReadAffy() ; myRMA <- justRMA() > > fit <- lmFit (myRMA, design) # Analysis design is in object, ?design? > > contrasts_matrix <- makeContrasts(Diseased-Healthy, levels = design) > > fit2 <- contrasts.fit (fit, contrasts_matrix) > > fit3 <- eBayes (fit2) > > test_results <- topTable(fit3, number=10, adjust="BH") > > # Then, I was uncertain regarding how to get the output with UniGene ID. > Wonder if a bit of tweaking in the function, probes2table should somehow > solve this ! > > # probes2table(****, featureNames(***), "hgu133a.db", anncols = > aaf.handler()[c(1,2,7,9)], html = FALSE, text = TRUE, filename = "****") > > Many thanks, > > Chintanu > > > > >> sessionInfo () >> > > R version 2.9.2 (2009-08-24) > > i386-pc-mingw32 > > locale: > > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > > [1] grDevices datasets splines graphics stats tcltk utils > methods base > > other attached packages: > > [1] annaffy_1.16.0 hgu133a.db_2.2.12 affycoretools_1.16.3 > KEGG.db_2.2.11 GO.db_2.2.11 RSQLite_0.7-2 > DBI_0.2-4 > > > [8] AnnotationDbi_1.6.1 limma_2.18.3 hgu133acdf_2.4.0 > affy_1.22.1 Biobase_2.4.1 survival_2.35-7 > > loaded via a namespace (and not attached): > > [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 > Category_2.10.1 gcrma_2.16.0 genefilter_1.24.2 > GOstats_2.10.0 > > [8] graph_1.22.2 GSEABase_1.6.1 preprocessCore_1.6.0 > RBGL_1.20.0 RCurl_1.2-0 tools_2.9.2 > XML_2.6-0 > > > [15] xtable_1.5-5 > > [[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