[BioC] Help with 'annotation' in GOHyeprGParamsClass

Marc Carlson mcarlson at fhcrc.org
Sat Nov 8 02:36:57 CET 2008


Hi Jason,

I have just merged a patch into place to fix this.  You should be able
to get a new version of both the annotate and Category packages soon
which should resolve this.  Please let me know if there are any other
issues.

  Marc


Jason Myers wrote:
> 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 at 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 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
>>
>>     
>
>
>
>



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