Dr. Gentleman,
I apologize for not providing an example.

############

> genes<-c("YAL038W", "YHL015W", "YNL178W", "YMR116C", "YBR031W") ##I
decreased the input size for example; error occurs for 191 genes too.
> test1<-new("GOHyperGParams",ontology="CC", conditional=FALSE,
geneIds=genes,annotation="org.Sc.sgd.db",categoryName="GO")
> test2<-hyperGTest(test1)

#############

ERROR:

Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
  variable "org.Sc.sgdENTREZID" was not found
Error in mget(probes, ID2EntrezID(datPkg)) :
  error in evaluating the argument 'envir' in selecting a method for
function 'mget'


> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
 methods   base

other attached packages:
 [1] SparseM_0.78        KEGG.db_2.2.5       org.Hs.eg.db_2.2.6
 org.Sc.sgd.db_2.2.6 GOstats_2.8.0
 [6] RBGL_1.18.0         GO.db_2.2.5         RSQLite_0.7-1       DBI_0.2-4
        Category_2.8.0
[11] genefilter_1.22.0   survival_2.34-1     annotate_1.20.0
xtable_1.5-4        graph_1.20.0
[16] AnnotationDbi_1.4.0 Biobase_2.2.0

loaded via a namespace (and not attached):
[1] GSEABase_1.4.0  XML_1.98-1      cluster_1.11.11 grid_2.8.0
 topGO_1.10.0

On Tue, Nov 4, 2008 at 3:32 PM, Robert Gentleman <rgentlem@fhcrc.org> wrote:

> Hi Jason,
>  The posting guide asks for a reproducible example, could you provide
> one? From that I can try and track down the issue.
>
>  best wishes
>   Robert
>
>
> Jason Myers wrote:
> > Dr. Gentleman,
> > I completed the update (see sessionInfo below).  However it seems as if
> part
> > of the org.Sc.sgd data package is missing (org.Sc.sgdENTREZID) or I need
> to
> > load an additional package.  The error I received is below.  Can you
> please
> > advise.
> >
> > Thanks,
> >
> > Jason
> >
> > "Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
> >   variable "org.Sc.sgdENTREZID" was not found"
> >
> >> sessionInfo()
> > R version 2.8.0 (2008-10-20)
> > i386-apple-darwin8.11.1
> >
> > locale:
> > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] splines   tools     stats     graphics  grDevices utils     datasets
> >  methods   base
> >
> > other attached packages:
> >  [1] org.Sc.sgd.db_2.2.6 GOstats_2.8.0       RBGL_1.18.0
> GO.db_2.2.5
> >         RSQLite_0.7-1
> >  [6] DBI_0.2-4           Category_2.8.0      genefilter_1.22.0
> > survival_2.34-1     annotate_1.20.0
> > [11] xtable_1.5-4        graph_1.20.0        AnnotationDbi_1.4.0
> > Biobase_2.2.0
> >
> > loaded via a namespace (and not attached):
> > [1] GSEABase_1.4.0  XML_1.98-1      cluster_1.11.11
> >
> > On Mon, Nov 3, 2008 at 7:23 PM, Robert Gentleman <rgentlem@fhcrc.org>
> wrote:
> >
> >> Hi Jason,
> >>  Your R (and hence Bioconductor) is out of date.  Please update to R
> >> 2.8.0 and Bioconductor 2.3.  Then you can use org.Sc.sgd.db for yeast
> >> (S. cerevisae annotations).
> >>
> >>  best wishes
> >>   Robert
> >>
> >> Jason Myers wrote:
> >>> Dear cateGOry experts,
> >>> hyperGTest documentation states that YEAST cannot be used as
> 'annotation'
> >>> when evaluating gene ontology representation status for a given set of
> >>> 'geneIds'.
> >>>
> >>> Because I am using a custom print I believe I need to create my own
> data
> >>> package to use as the annotation file for 'annotation'.  Can someone
> >> please
> >>> describe how to make a data package that will be compatible with the
> >>> 'annotation' required for proper function of hyperGTest?
> >>>
> >>> Session Info below,
> >>>
> >>> Thanks,
> >>>
> >>> Jason
> >>>
> >>>
> >>>> sessionInfo()
> >>> R version 2.6.2 (2008-02-08)
> >>> i386-apple-darwin8.10.1
> >>>
> >>> locale:
> >>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>>
> >>> attached base packages:
> >>> [1] splines   tools     stats     graphics  grDevices utils
> datasets
> >>>  methods   base
> >>>
> >>> other attached packages:
> >>>  [1] GOstats_2.4.0       RBGL_1.14.0         geneplotter_1.16.0
> >>>  lattice_0.17-4      limma_2.12.0
> >>>  [6] org.Sc.sgd.db_2.0.2 YEAST_2.0.1         GO.db_2.0.2
> >> DAAG_0.95
> >>>         MASS_7.2-40
> >>> [11] Category_2.4.0      genefilter_1.16.0   survival_2.34
> >>> annotate_1.16.1     xtable_1.5-2
> >>> [16] AnnotationDbi_1.0.6 RSQLite_0.6-4       DBI_0.2-4
> >>> graph_1.16.1        Biobase_1.16.3
> >>> [21] GO_2.0.1
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.9     grid_2.6.2
> >>>
> >>>
> >> --
> >> Robert Gentleman, PhD
> >> Program in Computational Biology
> >> Division of Public Health Sciences
> >> Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N, M2-B876
> >> PO Box 19024
> >> Seattle, Washington 98109-1024
> >> 206-667-7700
> >> rgentlem@fhcrc.org
> >>
> >
> >
> >
>
> --
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem@fhcrc.org
>



-- 
----------------------------------------
Jason Myers
650-387-2590
**NEW EMAIL ADDRESS**
dr.jason.myers@gmail.com
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