gmane.science.biology.informatics.conductor

GSEABase error in parsing msigdb_v2.5.xml

Hi,

I get error reading the last vesrsion of Broad msigdb . Is it supposed
to work?

> gss <- getBroadSets('/data/PathDB/msigdb_v2.5.xml')
Error: 'getBroadSets' failed to create gene sets:
  invalid BroadCollection category: 'c5'
> traceback()
6: stop("'getBroadSets' failed to create gene sets:\n  ",
conditionMessage(err), 
       call. = FALSE)
5: value[[3]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       geneSets <- unlist(mapply(.fromXML, uri, "//GENESET", factories, 
           SIMPLIFY = FALSE, USE.NAMES = FALSE))
   }, error = function(err) {
       stop("'getBroadSets' failed to create gene sets:\n  ",
conditionMessage(err), 
           call. = FALSE)
   })
1: getBroadSets("/data/PathDB/msigdb_v2.5.xml")
> packageDescription('GSEABase')
Package: GSEABase
Type: Package
Title: Gene set enrichment data structures and methods
Version: 1.2.0
Author: Martin Morgan, Seth Falcon, Robert Gentleman

(Continue reading)

headers

Martin Morgan | 15 May 19:46

Re: GSEABase error in parsing msigdb_v2.5.xml

Thanks Vladimir for the report, more below...

"Vladimir Morozov" <vmorozov@...> writes:

> Hi,
>  
> I get error reading the last vesrsion of Broad msigdb . Is it supposed
> to work?
>  
>> gss <- getBroadSets('/data/PathDB/msigdb_v2.5.xml')
> Error: 'getBroadSets' failed to create gene sets:
>   invalid BroadCollection category: 'c5'

The Broad added a category; I've updated GSEABase in both the devel
and release branches. The update should be available with biocLite
after 12 noon Friday; look for GSEABase 1.2.1 in the release.

One aspect that is a little unsatisfactory is that the subcategories
(CC/ BP/MF for c5, for instance) are not encoded in the XML, and so
are not present in the gene sets.

Martin

>> traceback()
> 6: stop("'getBroadSets' failed to create gene sets:\n  ",
> conditionMessage(err), 
>        call. = FALSE)
> 5: value[[3]](cond)
> 4: tryCatchOne(expr, names, parentenv, handlers[[1]])
> 3: tryCatchList(expr, classes, parentenv, handlers)

(Continue reading)