Help with 'annotation' in GOHyeprGParamsClass
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Jason Myers ▴ 50
@jason-myers-3115
Last seen 10.2 years ago
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 -- ---------------------------------------- Jason Myers 650-387-2590 **NEW EMAIL ADDRESS** dr.jason.myers@gmail.com ---------------------------------------- [[alternative HTML version deleted]]
Annotation GO Yeast Category Annotation GO Yeast Category • 1.5k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.6 years ago
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Hi Jason, Your R (and hence Bioconductor) is out of date.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
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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@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@fhcrc.org > -- ---------------------------------------- Jason Myers 650-387-2590 **NEW EMAIL ADDRESS** dr.jason.myers@gmail.com ---------------------------------------- [[alternative HTML version deleted]]
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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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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@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@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@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@fhcrc.org > -- ---------------------------------------- Jason Myers 650-387-2590 **NEW EMAIL ADDRESS** dr.jason.myers@gmail.com ---------------------------------------- [[alternative HTML version deleted]]
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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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Marc, Thanks for your help. How do I get the patch? On Fri, Nov 7, 2008 at 5:36 PM, Marc Carlson <mcarlson@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@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@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@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@fhcrc.org > >> > >> > > > > > > > > > > -- ---------------------------------------- Jason Myers 650-387-2590 **NEW EMAIL ADDRESS** dr.jason.myers@gmail.com ---------------------------------------- [[alternative HTML version deleted]]
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you can use biocLite or you can check out the updates using subversion, some details are here http://wiki.fhcrc.org/bioc/DeveloperPage/ 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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works great now. Thanks! On Sat, Nov 8, 2008 at 10:35 PM, Robert Gentleman <rgentlem@fhcrc.org>wrote: > you can use biocLite > or you can check out the updates using subversion, > some details are here > http://wiki.fhcrc.org/bioc/DeveloperPage/ > > > > 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@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@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@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@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@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@fhcrc.org > -- ---------------------------------------- Jason Myers 650-387-2590 **NEW EMAIL ADDRESS** dr.jason.myers@gmail.com ---------------------------------------- [[alternative HTML version deleted]]
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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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