Hello I am trying to apply a function to each element of a GeneSetCollection object. I have a problem preserving the data class, if I use lapply(). Is using a for loop my only option? Thanks for any help -burak Here's what I do: > gsc GeneSetCollection names: chr16q, chr5q23, ..., INOSITOL_OR_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITY (5452 total) unique identifiers: CMAR, USP10, ..., UCHL5IP (39655 total) types in collection: geneIdType: SymbolIdentifier (1 total) collectionType: BroadCollection (1 total) > test1 = GeneSetCollection(gsc[[1]],gsc[[2]]) > test1 GeneSetCollection names: chr16q, chr5q23 (2 total) unique identifiers: CMAR, USP10, ..., LOC728586 (91 total) types in collection: geneIdType: SymbolIdentifier (1 total) collectionType: BroadCollection (1 total) > lapply(test1,function(f) {geneIds(f) = "burak";return(f)}) [[1]] setName: chr16q geneIds: burak (total: 1) geneIdType: Symbol collectionType: Broad bcCategory: c1 (Positional) bcSubCategory: NA details: use 'details(object)' [[2]] setName: chr5q23 geneIds: burak (total: 1) geneIdType: Symbol collectionType: Broad bcCategory: c1 (Positional) bcSubCategory: NA details: use 'details(object)' ## returns a list > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] grDevices datasets splines graphics stats utils tools [8] methods base other attached packages: [1] org.Hs.eg.db_2.2.6 RSQLite_0.7-1 GSEABase_1.4.0 [4] graph_1.20.0 annotate_1.20.0 xtable_1.5-4 [7] AnnotationDbi_1.4.1 RMySQL_0.6-1 DBI_0.2-4 [10] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.0 [13] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 [16] Biobase_2.2.0 loaded via a namespace (and not attached): [1] affyio_1.10.1 cluster_1.11.11 preprocessCore_1.4.0 [4] XML_1.98-1 [[alternative HTML version deleted]]

Hi Burak, How about: GeneSetCollection(lapply(test1, function(f) {geneIds(f) = "burak";return(f)})) Works well with me: GeneSetCollection names: chr16q, chr5q23 (2 total) unique identifiers: burak (1 total) types in collection: geneIdType: SymbolIdentifier (1 total) collectionType: BroadCollection (1 total) Francois burak kutlu wrote: > Hello > I am trying to apply a function to each element of a GeneSetCollection object. I have a problem preserving the data class, if I use lapply(). Is using a for loop my only option? > Thanks for any help > -burak > > Here's what I do: > >> gsc > GeneSetCollection > names: chr16q, chr5q23, ..., INOSITOL_OR_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITY (5452 total) > unique identifiers: CMAR, USP10, ..., UCHL5IP (39655 total) > types in collection: > geneIdType: SymbolIdentifier (1 total) > collectionType: BroadCollection (1 total) > >> test1 = GeneSetCollection(gsc[[1]],gsc[[2]]) >> test1 > GeneSetCollection > names: chr16q, chr5q23 (2 total) > unique identifiers: CMAR, USP10, ..., LOC728586 (91 total) > types in collection: > geneIdType: SymbolIdentifier (1 total) > collectionType: BroadCollection (1 total) > >> lapply(test1,function(f) {geneIds(f) = "burak";return(f)}) > [[1]] > setName: chr16q > geneIds: burak (total: 1) > geneIdType: Symbol > collectionType: Broad > bcCategory: c1 (Positional) > bcSubCategory: NA > details: use 'details(object)' > > [[2]] > setName: chr5q23 > geneIds: burak (total: 1) > geneIdType: Symbol > collectionType: Broad > bcCategory: c1 (Positional) > bcSubCategory: NA > details: use 'details(object)' > > ## returns a list > >> sessionInfo() > R version 2.8.0 (2008-10-20) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] grDevices datasets splines graphics stats utils tools > [8] methods base > > other attached packages: > [1] org.Hs.eg.db_2.2.6 RSQLite_0.7-1 GSEABase_1.4.0 > [4] graph_1.20.0 annotate_1.20.0 xtable_1.5-4 > [7] AnnotationDbi_1.4.1 RMySQL_0.6-1 DBI_0.2-4 > [10] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.0 > [13] genefilter_1.22.0 survival_2.34-1 affy_1.20.0 > [16] Biobase_2.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 cluster_1.11.11 preprocessCore_1.4.0 > [4] XML_1.98-1 > > > > [[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