I am new to R/BioC. I am trying to do GO-based clustering of genes. The input (for the package csbl.go) needs to be gene name and GO terms in each row. Example: AP4B1 GO:0005215 GO:0005488 GO:0005515 GO:0005625 BCAS2 GO:0005515 GO:0005634 GO:0005681 GO:0008380 I tried using annotate in bioconductor: library("rat2302.db") library(annotate) testid<-c("1367462_at","1380262_at", "1392516_a_at", "1396521_at") goid1 <- rat2302GO[testid] But I get only each GO term in seperate row: toTable(goid1) probe_id go_id Evidence Ontology 1 1367462_at GO:0008152 IEA BP 2 1367462_at GO:0008152 ISO BP 3 1367462_at GO:0006508 IMP BP 4 1367462_at GO:0005886 IEA CC 5 1367462_at GO:0005737 IEA CC 6 1380262_at GO:0005575 ND CC 7 1380262_at GO:0005634 IEA CC 8 1380262_at GO:0005737 IEA CC 9 1367462_at GO:0005509 IEA MF 10 1367462_at GO:0005509 TAS MF Is there any easier way to get all GO terms per gene/probe? Any help is greatly appreciated. Thanks Rafi -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] csbl.go_1.4.0 RUnit_0.4.26 cluster_1.14.2 GO.db_2.7.1 BiocInstaller_1.4.9 [6] annotate_1.34.1 rat2302.db_2.7.1 org.Rn.eg.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 [11] AnnotationDbi_1.18.1 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] IRanges_1.14.4 stats4_2.15.0 tools_2.15.0 XML_3.9-4.1 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.

Hi Rafi, On 10/23/2012 6:59 PM, Rafi [guest] wrote: > I am new to R/BioC. I am trying to do GO-based clustering of genes. The input (for the package csbl.go) needs to be gene name and GO terms in each row. Example: Hmm. Weird that this package doesn't have facilities to do this. Anyway, not that difficult, starting after your line that creates the testid object: d.f <- select(rat2302.db, testid, c("SYMBOL", "GO")) out <- data.frame(tapply(d.f$GO, d.f$SYMBOL, paste, collapse = " ")) ## note there is a space between the " ". write.table(out, "input_for_csbl.txt", col.names = FALSE, quote = FALSE) Best, Jim > > AP4B1 GO:0005215 GO:0005488 GO:0005515 GO:0005625 > BCAS2 GO:0005515 GO:0005634 GO:0005681 GO:0008380 > > I tried using annotate in bioconductor: > > library("rat2302.db") > library(annotate) > testid<-c("1367462_at","1380262_at", "1392516_a_at", "1396521_at") > goid1<- rat2302GO[testid] > > But I get only each GO term in seperate row: > > toTable(goid1) > > probe_id go_id Evidence Ontology > 1 1367462_at GO:0008152 IEA BP > 2 1367462_at GO:0008152 ISO BP > 3 1367462_at GO:0006508 IMP BP > 4 1367462_at GO:0005886 IEA CC > 5 1367462_at GO:0005737 IEA CC > 6 1380262_at GO:0005575 ND CC > 7 1380262_at GO:0005634 IEA CC > 8 1380262_at GO:0005737 IEA CC > 9 1367462_at GO:0005509 IEA MF > 10 1367462_at GO:0005509 TAS MF > > Is there any easier way to get all GO terms per gene/probe? > > Any help is greatly appreciated. > > Thanks > Rafi > > -- output of sessionInfo(): > > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] csbl.go_1.4.0 RUnit_0.4.26 cluster_1.14.2 GO.db_2.7.1 BiocInstaller_1.4.9 > [6] annotate_1.34.1 rat2302.db_2.7.1 org.Rn.eg.db_2.7.1 RSQLite_0.11.1 DBI_0.2-5 > [11] AnnotationDbi_1.18.1 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 stats4_2.15.0 tools_2.15.0 XML_3.9-4.1 xtable_1.7-0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099