[BioC] GSEABase error parsing msigdb_v4.0.xml

Martin Morgan mtmorgan at fhcrc.org
Thu Nov 7 05:54:48 CET 2013

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,



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


This will upgrade _all_ your packages. If you're using an older version of R, 
then update R first.


> M Ng
> 	[[alternative HTML version deleted]]
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