Encountering error when using GOstats package
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Rich Savage ▴ 60
@rich-savage-3040
Last seen 9.2 years ago
University of Warwick, UK
Hi all, I'm using the GOstats package to find significant GO terms. This has been working fine but I've just upgraded to the R version 2.7.2 (and the latest versions of the Bioconductor packages) and I now get an error. I've had no luck trying to fix this and so am hoping someone an help me! EXAMPLE CODE: library(GO.db); library(GOstats); library(ath1121501.db); geneIDs <- c("AT1G21670","AT4G19960","AT5G37600","AT1G56220","AT1G53310") params <- new("GOHyperGParams", geneIds=geneIDs, annotation="ath1121501.db", ontology='MF', pvalueCutoff=0.05, conditional=TRUE, testDirection = "over"); hgTestResult <- hyperGTest(params); WHICH PRODUCES AN ERROR WHEN RUNNING THE "hyperGTest" FUNCTION: Error in get(mapName, envir = pkgEnv, inherits = FALSE) : variable "ath1121501ENTREZID" was not found Error in mget(probes, ID2EntrezID(datPkg)) : error in evaluating the argument 'envir' in selecting a method for function 'mget' TRACEBACK 14: mget(probes, ID2EntrezID(datPkg)) 13: unlist(mget(probes, ID2EntrezID(datPkg))) 12: unique(unlist(mget(probes, ID2EntrezID(datPkg)))) 11: getUniverseHelper(probes, datPkg, entrezIds) 10: getUniverseViaGo(p) 9: universeBuilder(p) 8: universeBuilder(p) 7: is(object, Cl) 6: is(object, Cl) 5: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", "hyperGTest") 4: hyperGTest(params) SESSION INFO R version 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] ath1121501_2.2.0 ath1121501cdf_2.2.0 ath1121501.db_2.2.0 GOstats_2.6.0 Category_2.6.0 genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 annotate_1.18.0 [10] xtable_1.5-3 graph_1.18.1 GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 I'd be very grateful for any help you can offer! Many thanks, Rich -- ------------------------------------------------------------------ Dr. Richard Savage Tel: +44 (0)24 765 50243 Systems Biology Centre University of Warwick Coventry CV4 7AL United Kingdom Web: http://www.programming4scientists.com/ http://wsbc.warwick.ac.uk/~richsavage/
GO ath1121501 GOstats GO ath1121501 GOstats • 1.6k views
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@vincent-j-carey-jr-4
Last seen 9 weeks ago
United States
> locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] ath1121501_2.2.0 ath1121501cdf_2.2.0 ath1121501.db_2.2.0 GOstats_2.6.0 This sessionInfo shows both a "non-SQLite" package (ath1121501) and ath1121501.db i think you need to get rid of the non-SQLite version
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Hi Vincent, Thanks for your reply. I uninstalled the non-SQLite package using: > remove.packages('ath1121501') I then re-ran the code I posted. Still got the error :-( (new sessionInfo also posted below) Error in get(mapName, envir = pkgEnv, inherits = FALSE) : variable "ath1121501ENTREZID" 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 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] ath1121501.db_2.2.0 GOstats_2.6.0 Category_2.6.0 RBGL_1.16.0 graph_1.18.1 [6] GO.db_2.2.0 genefilter_1.20.0 survival_2.34-1 annotate_1.18.0 xtable_1.5-3 [11] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 Vincent Carey 525-2265 wrote: >> locale: >> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] ath1121501_2.2.0 ath1121501cdf_2.2.0 ath1121501.db_2.2.0 GOstats_2.6.0 > > This sessionInfo shows both a "non-SQLite" package (ath1121501) and ath1121501.db > > i think you need to get rid of the non-SQLite version > -- ------------------------------------------------------------------ Dr. Richard Savage Tel: +44 (0)24 765 50243 Systems Biology Centre University of Warwick Coventry CV4 7AL United Kingdom Web: http://www.programming4scientists.com/ http://wsbc.warwick.ac.uk/~richsavage/
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Hi Rich, Thanks for pointing this out, and sorry it does not work. It is another of the organisms that uses its own set of IDs, and I will need to modify the GOstats code to deal with it. Should be done by Monday (but only in the devel arm, using the R 2.8.0 candidate), best wishes Robert Rich Savage wrote: > Hi Vincent, > > Thanks for your reply. > > I uninstalled the non-SQLite package using: > > > remove.packages('ath1121501') > > I then re-ran the code I posted. Still got the error :-( > (new sessionInfo also posted below) > > > Error in get(mapName, envir = pkgEnv, inherits = FALSE) : > variable "ath1121501ENTREZID" 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 2.7.2 (2008-08-25) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] ath1121501.db_2.2.0 GOstats_2.6.0 Category_2.6.0 > RBGL_1.16.0 graph_1.18.1 > [6] GO.db_2.2.0 genefilter_1.20.0 survival_2.34-1 > annotate_1.18.0 xtable_1.5-3 > [11] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 > Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 > > > > Vincent Carey 525-2265 wrote: >>> locale: >>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] ath1121501_2.2.0 ath1121501cdf_2.2.0 ath1121501.db_2.2.0 >>> GOstats_2.6.0 >> >> This sessionInfo shows both a "non-SQLite" package (ath1121501) and >> ath1121501.db >> >> i think you need to get rid of the non-SQLite version >> > -- 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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> Hi Vincent, > > Thanks for your reply. > > I uninstalled the non-SQLite package using: > > > remove.packages('ath1121501') > > I then re-ran the code I posted. Still got the error :-( > (new sessionInfo also posted below) > > > Error in get(mapName, envir = pkgEnv, inherits = FALSE) : > variable "ath1121501ENTREZID" was not found > Error in mget(probes, ID2EntrezID(datPkg)) : > error in evaluating the argument 'envir' in selecting a method for function ok -- it seems that there are no Entrez Gene identifiers for arabadopsis defined in the ath1121501.db -- use ath1121501() to see what mappings are there. i personally do not know whether such mappings exist. i believe you will have to be more specific in your choice of the universe specification when creating the GOHyperGParams object. i do not see an org.* package for arabadop.
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Hi all, This issue is resolved. You need to be using R 2.8.0 release candidate and the devel version of the Category package which will deal with Arabidopsis arrays more gracefully. We are planning a few more improvements (hopefully before the next release). Please post any new issues that arise Robert Rich Savage wrote: > Hi Vincent, > > Thanks for your reply. > > I uninstalled the non-SQLite package using: > > > remove.packages('ath1121501') > > I then re-ran the code I posted. Still got the error :-( > (new sessionInfo also posted below) > > > Error in get(mapName, envir = pkgEnv, inherits = FALSE) : > variable "ath1121501ENTREZID" 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 2.7.2 (2008-08-25) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] ath1121501.db_2.2.0 GOstats_2.6.0 Category_2.6.0 > RBGL_1.16.0 graph_1.18.1 > [6] GO.db_2.2.0 genefilter_1.20.0 survival_2.34-1 > annotate_1.18.0 xtable_1.5-3 > [11] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 > Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 > > > > Vincent Carey 525-2265 wrote: >>> locale: >>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] ath1121501_2.2.0 ath1121501cdf_2.2.0 ath1121501.db_2.2.0 >>> GOstats_2.6.0 >> >> This sessionInfo shows both a "non-SQLite" package (ath1121501) and >> ath1121501.db >> >> i think you need to get rid of the non-SQLite version >> > -- 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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