R help - Nov 2008 - Help with 'annotation' in GOHyperGParamsClass

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

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

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Hi Jason,

There is a listserv dedicated to Bioconductor packages; I suggest you 
post there.

bioconductor at stat.math.ethz.ch

Best,

Jim



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
> 
-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662