Dear Bioc, I am using the package GSEABase, and I have the following error. I imput eset in the function GeneSetCollection, but I do retrive the following error. I am using Illumna datata, and transformed the lumi.batch in expression set. > gsc <- GeneSetCollection(eset, + setType = KEGGCollection() + ) Error in validObject(.Object) : invalid class "ScalarCharacter" object: ScalarCharacter must have length one thank you > 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] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] genefilter_1.22.0 GSEABase_1.4.0 graph_1.20.0 [4] ROC_1.16.0 maxstat_0.7-12 mvtnorm_0.9-2 [7] exactRankTests_0.8-17 survival_2.34-1 biomaRt_1.16.0 [10] limma_2.16.3 annaffy_1.14.0 KEGG.db_2.2.5 [13] GO.db_2.2.5 illuminaHumanv2.db_1.1.3 Mfuzz_1.12.0 [16] e1071_1.5-18 class_7.2-44 Heatplus_1.12.0 [19] lumi_1.8.3 RSQLite_0.7-1 DBI_0.2-4 [22] preprocessCore_1.4.0 mgcv_1.4-1 affy_1.20.0 [25] annotate_1.20.1 xtable_1.5-4 AnnotationDbi_1.4.1 [28] Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 cluster_1.11.11 RCurl_0.92-0 XML_1.98-1 [[alternative HTML version deleted]]

Hi John -- "John Lande" <john.lande77 at="" gmail.com=""> writes: > Dear Bioc, > > I am using the package GSEABase, and I have the following error. > I imput eset in the function GeneSetCollection, but I do retrive the > following error. I am using Illumna datata, > and transformed the lumi.batch in expression set. > >> gsc <- GeneSetCollection(eset, > + setType = KEGGCollection() > + ) > Error in validObject(.Object) : > invalid class "ScalarCharacter" object: ScalarCharacter must have length > one It's a little hard to know exactly what is going wrong for you; the output of traceback() might help. Also, GeneSetCollection creates a list of GeneSet's. R has this to say about the GeneSet class: > getClass("GeneSet") Class "GeneSet" Slots: Name: geneIdType geneIds setName Class: GeneIdentifierType character ScalarCharacter Name: setIdentifier shortDescription longDescription Class: ScalarCharacter ScalarCharacter ScalarCharacter Name: organism pubMedIds urls Class: ScalarCharacter character character Name: contributor version creationDate Class: character Versions character Name: collectionType Class: CollectionType Known Subclasses: "GeneColorSet" The error you see comes from one of setName, setIdentifier, shortDescription, longDescription, or organism being created with a character vector that is either empty or has more than 1 entry. My best guess is shortDescription, which comes from experimentData(eset)@title, or longDescription, from abstract(eset). Other possibilities: setName comes from the keys of the "PATH2PROBE" map in the organism you're using. Should be OK. setIdentifier should be auto-generated with GSEABase:::.uniqueIdentifier(). Should be OK. 'organism' comes from the 'annotation' slot of the ExpressionSet getAnnMap("ORGANISM", annotation(eset)) or is set to "" if there is no annotation information. Should be OK. Does that help? Martin > thank you > >> 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] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] genefilter_1.22.0 GSEABase_1.4.0 > graph_1.20.0 > [4] ROC_1.16.0 maxstat_0.7-12 > mvtnorm_0.9-2 > [7] exactRankTests_0.8-17 survival_2.34-1 > biomaRt_1.16.0 > [10] limma_2.16.3 annaffy_1.14.0 > KEGG.db_2.2.5 > [13] GO.db_2.2.5 illuminaHumanv2.db_1.1.3 > Mfuzz_1.12.0 > [16] e1071_1.5-18 class_7.2-44 > Heatplus_1.12.0 > [19] lumi_1.8.3 RSQLite_0.7-1 > DBI_0.2-4 > [22] preprocessCore_1.4.0 mgcv_1.4-1 > affy_1.20.0 > [25] annotate_1.20.1 xtable_1.5-4 > AnnotationDbi_1.4.1 > [28] Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 cluster_1.11.11 RCurl_0.92-0 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793