[BioC] Help with 'annotation' in GOHyeprGParamsClass

Robert Gentleman rgentlem at fhcrc.org
Sun Nov 9 07:35:20 CET 2008 

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Jason Myers wrote:
> Marc,
> Thanks for your help.  How do I get the patch?
> 
> On Fri, Nov 7, 2008 at 5:36 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> 
>> 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
>>>>
>>>>
>>>
>>>
>>>
>>
> 
> 

-- 
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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