[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

[Jenny Drnevich]

Hi Herve,

Thanks for looking into this. Unfortunately, your fix didn't quite work:


>You can compute the ath1121501ACCNUM yourself with:
>
> > ath1121501ACCNUM <- eapply(ath1121501MULTIHIT,
>                              function(ids) if (length(ids) > 1) 
> "multiple" else ids)

This changes ath1121501ACCNUM from an environment to a list, and to 
use hyperGTest(), it needs to be an environment. I know very little 
about environments, and the simple as.environment() didn't work, so I 
don't know how to fix it.

Thanks,
Jenny



>Let me know if you find any other problem.
>
>Thanks!
>H.
>
>
> >
> > Thanks,
> > Jenny
> >
> >> sessionInfo()
> > R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] splines   tools     stats     graphics  grDevices utils     datasets
> > [8] methods   base
> >
> > other attached packages:
> >  [1] limma_2.11.13        ath1121501_1.99.10   GOstats_2.3.17
> >  [4] Category_2.3.39      genefilter_1.15.11   survival_2.32
> >  [7] RBGL_1.13.6          annotate_1.15.11     xtable_1.5-1
> > [10] GO.db_1.99.3         AnnotationDbi_0.99.1 RSQLite_0.6-2
> > [13] DBI_0.2-3            graph_1.15.20        Biobase_1.15.34
> >
> > loaded via a namespace (and not attached):
> > [1] cluster_1.11.7     simpleaffy_2.13.01
> >
> >
> >
> >
> >
> > Jenny Drnevich, Ph.D.
> >
> > Functional Genomics Bioinformatics Specialist
> > W.M. Keck Center for Comparative and Functional Genomics
> > Roy J. Carver Biotechnology Center
> > University of Illinois, Urbana-Champaign
> >
> > 330 ERML
> > 1201 W. Gregory Dr.
> > Urbana, IL 61801
> > USA
> >
> > ph: 217-244-7355
> > fax: 217-265-5066
> > e-mail: drnevich at uiuc.edu