[BioC] Help with 'annotation' in GOHyeprGParamsClass
mcarlson at fhcrc.org
mcarlson at fhcrc.org
Mon Nov 10 19:39:48 CET 2008
Hi Jason,
Updated packages are available on the bioconductor website and
biocLite works as well.
Marc
Quoting Jason Myers <dr.jason.myers at gmail.com>:
> 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
>> >>
>> >>
>> >
>> >
>> >
>> >
>>
>>
>
>
> --
> ----------------------------------------
> Jason Myers
> 650-387-2590
> **NEW EMAIL ADDRESS**
> dr.jason.myers at gmail.com
> ----------------------------------------
>
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