GOstats error
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@sebastien-gerega-2229
Last seen 8.1 years ago
Hi, Today I received the following error while using GOstats: > hgOver Gene to GO MF test for over-representation 315 GO MF ids tested (15 have p < 0.01) Selected gene set size: 107 Gene universe size: 7005 Annotation package: lumiHumanAll > summary(hgOver) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "GO:0001584" not found Any idea what could be causing this? or the best way to work around it? Session info at the bottom. Thanks, Sebastien > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia. 1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.2.11 gplots_2.7.1 caTools_1.9 bitops_1.0-4.1 [5] gdata_2.6.1 gtools_2.6.1 xtable_1.5-5 biomaRt_2.0.0 [9] genefilter_1.24.2 KEGG.db_2.2.11 GOstats_2.10.0 graph_1.22.2 [13] Category_2.10.1 limma_2.18.3 lumiHumanIDMapping_1.2.1 lumiHumanAll.db_1.6.1 [17] GDD_0.1-13 lumi_1.10.1 RSQLite_0.7-2 DBI_0.2-4 [21] preprocessCore_1.6.0 mgcv_1.5-5 affy_1.22.1 annotate_1.22.0 [25] AnnotationDbi_1.6.1 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 GSEABase_1.6.1 lattice_0.17-25 nlme_3.1-93 RBGL_1.20.0 RCurl_0.98-1 splines_2.9.1 [8] survival_2.35-5 tools_2.9.1 XML_2.5-1
Annotation GO Annotation GO • 676 views
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Al Ivens ▴ 30
@al-ivens-3203
Last seen 8.1 years ago
Hi Sebastien, I have had this problem before too. It is due to the fact that some GO terms are obsolete: GO:0001584 rhodopsin-like receptor activity. OBSOLETE. A G-protein coupled receptor that is structurally/functionally related to the rhodopsin receptor. ... As an interim work-around, I check the GO term annotations for each locus being enrichment tested, and remove those GO terms that are not in GO.db. However, I am sure someone else will have a more elegant solution to this problem! Cheers, al > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Sebastien Gerega > Sent: 02 September 2009 06:52 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] GOstats error > > > Hi, > Today I received the following error while using GOstats: > > > hgOver > Gene to GO MF test for over-representation > 315 GO MF ids tested (15 have p < 0.01) > Selected gene set size: 107 > Gene universe size: 7005 > Annotation package: lumiHumanAll > > summary(hgOver) > Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : > value for "GO:0001584" not found > > Any idea what could be causing this? or the best way to work > around it? > > Session info at the bottom. > > Thanks, > Sebastien > > > > > sessionInfo() > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1 > 252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=En > glish_Australia.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] GO.db_2.2.11 gplots_2.7.1 > caTools_1.9 bitops_1.0-4.1 > [5] gdata_2.6.1 gtools_2.6.1 > xtable_1.5-5 biomaRt_2.0.0 > [9] genefilter_1.24.2 KEGG.db_2.2.11 > GOstats_2.10.0 graph_1.22.2 > [13] Category_2.10.1 limma_2.18.3 > lumiHumanIDMapping_1.2.1 lumiHumanAll.db_1.6.1 > [17] GDD_0.1-13 lumi_1.10.1 > RSQLite_0.7-2 DBI_0.2-4 > [21] preprocessCore_1.6.0 mgcv_1.5-5 > affy_1.22.1 annotate_1.22.0 > [25] AnnotationDbi_1.6.1 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 GSEABase_1.6.1 lattice_0.17-25 nlme_3.1-93 > RBGL_1.20.0 RCurl_0.98-1 splines_2.9.1 > [8] survival_2.35-5 tools_2.9.1 XML_2.5-1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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