Hi Paul,

If I remember correctly, the hypergeometric test (for GO at least) was split
into two different packages, Category and GOstats. You also need to load the
GOstats package where the GOHyperGResult class is defined. Try loading this
package to see if that does not solve the problem.

Cheers,
--Tony

On Feb 4, 2008 4:05 AM, Paul Shannon <ptshannon@speakeasy.net> wrote:

> Hi all,
>
> I have encountered a puzzling problem with the ever-reliable
> hyperGTest function.  It
> runs the usual amount of time (30 or more seconds) and then fails
> with the message
> that 'GOHyperGResult' is not defined.    Here is the whole of my
> session, with sessionInfo
> attached.
>
> Any ideas?  Thanks!
>
>  - Paul
>
>  > library (Category)
>  > library (org.Hs.eg.db)
>  > library (GO)
>  > genes = c ("8038", "259", "51529", "164", "335", "336", "338", "341")
>  > params = new ("GOHyperGParams", geneIds=genes,
> annotation='org.Hs.eg.db', ontology='BP')
>  > hgr.bp = hyperGTest (params)
> Error in getClass(Class, where = topenv(parent.frame())) :
>   c("\"GOHyperGResult\" is not a defined class", "\"BPHyperGResult\"
> is not a defined class")
>  > sessionInfo ()
> R version 2.6.1 (2007-11-26)
> i386-apple-darwin8.10.1
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages:
>  [1] GO_1.17.0           org.Hs.eg.db_2.0.2  Category_2.4.0
> genefilter_1.16.0   survival_2.34       annotate_1.16.0     xtable_1.5-1
>  [8] AnnotationDbi_1.0.6 RSQLite_0.6-2       DBI_0.2-3
> graph_1.15.17       Biobase_1.16.0
>
> loaded via a namespace (and not attached):
> [1] RBGL_1.13.6    cluster_1.11.9
>
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