[BioC] Error with GeneSetCollection - Pfam or Chrloc

[Martin Morgan]

Hi James --

James Wagner <jamesrwagner at gmail.com> writes:

> Hello, I am trying to obtain a GeneSetCollection (package GSEABase)
> corresponding to an experiment using the hgu95a annotation.
>
> When I use for example, the KEGG gene set collection, the mapping and
> creation of the GeneSetCollection object takes place without issue:
>
> gsc <- GeneSetCollection(eset, setType=KEGGCollection())
>
> On the other hand when I enter:
>
>> gsc <- GeneSetCollection(eset, setType=PfamCollection())
>
> I get:
>
> Error in `direction<-`(`*tmp*`, value = -1L) :
>   changing the direction of an "IpiAnnDbMap" object is not supported
>
> Similarly for:
>
>> gsc <- GeneSetCollection(eset, setType=ChrlocCollection())
>
> I get:
>
> Error in `direction<-`(`*tmp*`, value = -1L) :
>   changing the direction of an "AnnDbMap" object is not supported

These are definitely shortcomings in GSEABase, and I'll work to get a
fix in place over the next couple of days.

Martin

> Is there any help that anyone can give me for how to correct this issue?
>
> Here is some version information, in case it matters:
>
> platform       powerpc-apple-darwin8.11.1
> arch           powerpc
> os             darwin8.11.1
> system         powerpc, darwin8.11.1
> status
> major          2
> minor          8.0
> year           2008
> month          10
> day            20
> svn rev        46754
> language       R
> version.string R version 2.8.0 (2008-10-20)
>
> Thanks,
>
> James Wagner
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Phone: (206) 667-2793