GSEABase error parsing msigdb

GSEABase error parsing msigdb_v3.1.xml

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Lina Hultin-Rosenberg ▴ 80

@lina-hultin-rosenberg-2207

Last seen 9.6 years ago

Dear list, I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to that Broad added another category (c6). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c5, or an alternative way to get all categories? See the R code and versions below. Thank you! Best regards, Lina Hultin Rosenberg PhD student Karolinska Institutet Stockholm, Sweden ###################################################################### ####### > library(GSEABase) > msigdb.file = system.file("extdata", "msigdb_v3.1.xml", package="GSEABase") > broad.genesets = GeneSet(BroadCollection(), urls=msigdb.file) Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'c6' > packageDescription("GSEABase") Package: GSEABase Type: Package Title: Gene set enrichment data structures and methods Version: 1.20.1 Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer: Bioconductor Package Maintainer <maintainer at="" bioconductor.org=""> Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). License: Artistic-2.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, methods, XML LazyLoad: yes biocViews: Infrastructure, Bioinformatics Collate: utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R methods-CollectionType.R methods-ExpressionSet.R methods- GeneColorSet.R methods-GeneIdentifierType.R ..... Packaged: 2012-11-25 06:15:25 UTC; biocbuild Built: R 2.15.2; ; 2012-11-25 12:32:24 UTC; windows -- File: C:/Program Files/R/R-2.15.2/library/GSEABase/Meta/package.rds >

GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO • 1.6k views

ADD COMMENT • link updated 11.2 years ago by Martin Morgan 25k • written 11.2 years ago by Lina Hultin-Rosenberg ▴ 80

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 days ago

United States

On 01/31/2013 02:37 AM, Lina Hultin-Rosenberg wrote: > Dear list, > > I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to that Broad added another category (c6). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c5, or an alternative way to get all categories? > > See the R code and versions below. > > Thank you! thank you for the report; this is updated in version 1.20.2, which should be available Friday at 10am ish Seattle time. The only way to import a single category is to use just a subset of the original data in its XML representation downloaded from http://www.broadinstitute.org/gsea/downloads.jsp, as hinted at on ?getObjects help page. Hope that helps, Martin > > > Best regards, > > Lina Hultin Rosenberg > PhD student > Karolinska Institutet > Stockholm, Sweden > > #################################################################### ######### > > library(GSEABase) >> msigdb.file = system.file("extdata", "msigdb_v3.1.xml", package="GSEABase") >> broad.genesets = GeneSet(BroadCollection(), urls=msigdb.file) > Error: 'getBroadSets' failed to create gene sets: > invalid BroadCollection category: 'c6' >> packageDescription("GSEABase") > Package: GSEABase > Type: Package > Title: Gene set enrichment data structures and methods > Version: 1.20.1 > Author: Martin Morgan, Seth Falcon, Robert Gentleman > Maintainer: Bioconductor Package Maintainer <maintainer at="" bioconductor.org=""> > Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). > License: Artistic-2.0 > Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph > Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz > Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, methods, XML > LazyLoad: yes > biocViews: Infrastructure, Bioinformatics > Collate: utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R methods-CollectionType.R methods-ExpressionSet.R methods- GeneColorSet.R methods-GeneIdentifierType.R ..... > Packaged: 2012-11-25 06:15:25 UTC; biocbuild > Built: R 2.15.2; ; 2012-11-25 12:32:24 UTC; windows > > -- File: C:/Program Files/R/R-2.15.2/library/GSEABase/Meta/package.rds >> > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD COMMENT • link 11.2 years ago Martin Morgan 25k

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Thanks a lot for the help and information! Best, Lina -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: den 31 januari 2013 14:35 To: Lina Hultin-Rosenberg Cc: bioconductor at r-project.org Subject: Re: [BioC] GSEABase error parsing msigdb_v3.1.xml On 01/31/2013 02:37 AM, Lina Hultin-Rosenberg wrote: > Dear list, > > I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to that Broad added another category (c6). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c5, or an alternative way to get all categories? > > See the R code and versions below. > > Thank you! thank you for the report; this is updated in version 1.20.2, which should be available Friday at 10am ish Seattle time. The only way to import a single category is to use just a subset of the original data in its XML representation downloaded from http://www.broadinstitute.org/gsea/downloads.jsp, as hinted at on ?getObjects help page. Hope that helps, Martin > > > Best regards, > > Lina Hultin Rosenberg > PhD student > Karolinska Institutet > Stockholm, Sweden > > #################################################################### ######### > > library(GSEABase) >> msigdb.file = system.file("extdata", "msigdb_v3.1.xml", >> package="GSEABase") broad.genesets = GeneSet(BroadCollection(), >> urls=msigdb.file) > Error: 'getBroadSets' failed to create gene sets: > invalid BroadCollection category: 'c6' >> packageDescription("GSEABase") > Package: GSEABase > Type: Package > Title: Gene set enrichment data structures and methods > Version: 1.20.1 > Author: Martin Morgan, Seth Falcon, Robert Gentleman > Maintainer: Bioconductor Package Maintainer > <maintainer at="" bioconductor.org=""> > Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). > License: Artistic-2.0 > Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), > annotate, methods, graph > Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz > Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, > methods, XML > LazyLoad: yes > biocViews: Infrastructure, Bioinformatics > Collate: utilities.R AAA.R AllClasses.R AllGenerics.R getObjects.R methods-CollectionType.R methods-ExpressionSet.R methods- GeneColorSet.R methods-GeneIdentifierType.R ..... > Packaged: 2012-11-25 06:15:25 UTC; biocbuild > Built: R 2.15.2; ; 2012-11-25 12:32:24 UTC; windows > > -- File: C:/Program Files/R/R-2.15.2/library/GSEABase/Meta/package.rds >> > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

ADD REPLY • link 11.2 years ago Lina Hultin-Rosenberg ▴ 80

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