Help with 'annotation' in GOHyeprGParamsClass
1
0
Entering edit mode
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
ADD COMMENT •
0
Entering edit mode
rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.6 years ago
United States
Hi Jason, Your R (and hence Bioconductor) is out of date.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
ADD COMMENT •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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 >> >> > > > >
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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 > ---------------------------------------- >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 776 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6