Hi All, I noticed a problem which I am not sure if I miss something. I attempt to select GO terms in the biological process categories (BP). But for some reasons the filtering seems not working. One id is in the MF category, but still is selected (see below). library(GSEABase) data(sample.ExpressionSet) gg <- GeneSetCollection(sample.ExpressionSet[200:250], setType = GOCollection(ontology="BP")) goId = "GO:0003676" # is in MF, not in BP goId %in% names(gg) TRUE > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 KEGG.db_2.3.5 [4] Category_2.12.0 GO.db_2.3.5 GSEABase_1.8.0 [7] graph_1.24.1 annotate_1.24.0 mouse4302.db_2.3.5 [10] org.Mm.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-5 [13] AnnotationDbi_1.8.1 genefilter_1.28.2 ALL_1.4.7 [16] Biobase_2.6.1 loaded via a namespace (and not attached): [1] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 [5] XML_2.6-0 xtable_1.5-6 > Thanks for looking into this. Jason

Hi Jason, the help page of GeneSetCollection specifies that using 'ontology' does work like 'evidence' where filtering is taking place. You could filter out your results using GOTERM (GO.db) in this way: goId %in% names(gg[lapply(mget(names(gg), GOTERM), Ontology) == "MF"]) ##[1] TRUE goId %in% names(gg[lapply(mget(names(gg), GOTERM), Ontology) == "BP"]) HTH, J. On 29/03/2010 18:41, Jason Lu wrote: > Hi All, > > I noticed a problem which I am not sure if I miss something. > > I attempt to select GO terms in the biological process categories > (BP). But for some reasons the filtering seems not working. One id is > in the MF category, but still is selected (see below). > > > library(GSEABase) > data(sample.ExpressionSet) > gg<- GeneSetCollection(sample.ExpressionSet[200:250], > setType = GOCollection(ontology="BP")) > > goId = "GO:0003676" # is in MF, not in BP > > goId %in% names(gg) > TRUE > >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 KEGG.db_2.3.5 > [4] Category_2.12.0 GO.db_2.3.5 GSEABase_1.8.0 > [7] graph_1.24.1 annotate_1.24.0 mouse4302.db_2.3.5 > [10] org.Mm.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-5 > [13] AnnotationDbi_1.8.1 genefilter_1.28.2 ALL_1.4.7 > [16] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 > [5] XML_2.6-0 xtable_1.5-6 >> > > Thanks for looking into this. > > Jason > > _______________________________________________ > 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 >