*Hi,* *I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to Broad adding another category (c7). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c6, or an alternative way to get all categories?* > gsc = getBroadSets("msigdb_v4.0.xml") *Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'c7'* Many thanks, M Ng [[alternative HTML version deleted]]

On 11/06/2013 08:48 PM, Milica Ng wrote: > *Hi,* > > *I am getting an error when trying to parse the latest msigdb version from > Broad. I suspect the problem is due to Broad adding another category (c7). > Will the new category be included in GSEABase? Is there a way to parse only > categories c1-c6, or an alternative way to get all categories?* > >> gsc = getBroadSets("msigdb_v4.0.xml") > > *Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection > category: 'c7'* > > Many thanks, From http://bioconductor.org/packages/release/bioc/news/GSEABase/NEWS This was fixed in version 1.23.1, so should be fixed in the current release 1.24.0. Perhaps you need to upgrade to the current release? If you're using R-3.0.1 or 3.0.2, you should be able to source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") This will upgrade _all_ your packages. If you're using an older version of R, then update R first. Martin > > M Ng > > [[alternative HTML version deleted]] > > _______________________________________________ > 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