[BioC] Help with 'annotation' in GOHyeprGParamsClass

[Robert Gentleman]

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  Your R (and hence Bioconductor) is out of date.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 at fhcrc.org