[BioC] Help with 'annotation' in GOHyeprGParamsClass

[Robert Gentleman]

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  Your R (and hence Bioconductor) is out of date.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