GSEABase error parsing msigdb_v3.1.xml
1
0
Entering edit mode
@lina-hultin-rosenberg-2207
Last seen 8.1 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 • 1.2k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 17 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
0
Entering edit mode
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

Login before adding your answer.

Traffic: 312 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6