Question: GSEABase - mapIdentifiers
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gravatar for Hans-Ulrich Klein
11.7 years ago by
United States
Hans-Ulrich Klein330 wrote:
Hello all, the function mapIdentifiers() works fine for "GeneSet" objects whereas it throws an error message when a "GeneColorSet" is given: > library("GSEABase") > gs = GeneColorSet(geneIds=c("TYMP", "XPO1", "LBR"), geneIdType=SymbolIdentifier(), setName="testlist", shortDescription="blabla", phenotype="pheno data", geneColor = factor(c("increase","increase","increase")), phenotypeColor = factor(c("A","B","A"))) > gs2 = mapIdentifiers(gs, AnnotationIdentifier("hgu95av2")) Error in validObject(.Object) : invalid class "GeneColorSet" object: gene and color lengths differ It seems that there is a problem when the number of genes/probes in the set changes. Regards, Hans-Ulrich > sessionInfo() R version 2.6.2 (2008-02-08) x86_64-pc-linux-gnu locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu95av2_2.0.1 Ruuid_1.16.1 GSEABase_1.0.3 [4] AnnotationDbi_1.0.6 RSQLite_0.6-8 DBI_0.2-4 [7] Biobase_1.16.3 loaded via a namespace (and not attached): [1] XML_1.93-2 rcompgen_0.1-17
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ADD COMMENTlink modified 11.7 years ago by Martin Morgan ♦♦ 24k • written 11.7 years ago by Hans-Ulrich Klein330
Answer: GSEABase - mapIdentifiers
0
gravatar for Martin Morgan
11.7 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
Hans-Ulrich, Thank you very much for the bug report and reproducible example. This has been fixed in the development version of GSEABase, and will appear through biocLite after Friday at noon, Seattle time. An important caveat to using the development version is that the representation of GeneIdentifierTypes (e.g., SymbolIdentifier) have been changed, so that serialized (e.g., saved) instances of GeneSets and GeneColorSets might need to be updated. The update mechanism has not yet been thoroughly tested, so if you have saved gene sets that are not easily recreated you might wish to hold off on updating GSEABase. The reason for this change is partly motivated by GOCollections (which now know about ontology) and by the desire to map between, e.g., SymbolIdentifier and GenenameIdentifier without having to go through AnnotationIdentifier. The new mapping allows, for the gene set below geneIdType(gs) <- GenenameIdentifier("hgu95av2") (the 'hgu95av2' is new; previously this was only allowed in AnnotationIdentifier) which says to use the maps in the hgu95av2 annotation package to figure out how to get from Symbol to Genename. Thanks again for the report. Martin Hans-Ulrich Klein wrote: > Hello all, > > the function mapIdentifiers() works fine for "GeneSet" objects whereas > it throws an error message when a "GeneColorSet" is given: > > > library("GSEABase") > > gs = GeneColorSet(geneIds=c("TYMP", "XPO1", "LBR"), > geneIdType=SymbolIdentifier(), > setName="testlist", > shortDescription="blabla", > phenotype="pheno data", > geneColor = factor(c("increase","increase","increase")), > phenotypeColor = factor(c("A","B","A"))) > > > gs2 = mapIdentifiers(gs, AnnotationIdentifier("hgu95av2")) > Error in validObject(.Object) : > invalid class "GeneColorSet" object: gene and color lengths differ > > It seems that there is a problem when the number of genes/probes in the > set changes. > > Regards, > Hans-Ulrich > > > > > > sessionInfo() > R version 2.6.2 (2008-02-08) > x86_64-pc-linux-gnu > > locale: > C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] hgu95av2_2.0.1 Ruuid_1.16.1 GSEABase_1.0.3 > [4] AnnotationDbi_1.0.6 RSQLite_0.6-8 DBI_0.2-4 > [7] Biobase_1.16.3 > > loaded via a namespace (and not attached): > [1] XML_1.93-2 rcompgen_0.1-17 > > _______________________________________________ > 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
ADD COMMENTlink written 11.7 years ago by Martin Morgan ♦♦ 24k
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