error with display of significant nodes using topGO
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@kishor-tappita-2563
Last seen 8.1 years ago
Dear List, When trying to find the enriched GO terms using topGO. I get the below error when trying to display the significant nodes. The method works fine for MF . I get an error while computing enrichment for "BP" > showSigOfNodes(GOdata,score(resultKS.elim),firstTerms=5,useInfo="all") Error in subGraph(nodesInInducedGraph(dag, startNodes), dag) : invalid arg: snodes contains nodes not in the graph: GO:0003700, GO:0004984, GO:0005515, GO:0008083, GO:0042803 > sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rgraphviz_1.22.1 hgu133plus2.db_2.2.11 topGO_1.12.0 [4] SparseM_0.80 graph_1.22.2 GO.db_2.2.11 [7] RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.6.1 [10] limma_2.18.3 GEOquery_2.8.0 RCurl_0.98-1 [13] bitops_1.0-4.1 Biobase_2.4.1 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] kernlab_0.9-8 lattice_0.17-25 tools_2.9.2 XML_2.5-1 Thanks, kishor
GO hgu133plus2 topGO GO hgu133plus2 topGO • 1.8k views
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Adrian Alexa ▴ 400
@adrian-alexa-936
Last seen 8.1 years ago
Hi Kishor, can it be that the GOdata object and the resultKS.elim are incompatible? Did you obtain the resultKS.elim object from the GOdata object? I'm pretty sure that you build the resultKS.elim object using lets say BP ontology and then you build a new GOdata object for MF (or something similar). Another possibility is that you saved the resultKS.elim from a previous session and in the current session you build a topGOdata object which make use of the newly updated GO.db and then you will of course get a mismatch in the nodes names. Hope this helps, Adrian On Thu, Sep 17, 2009 at 11:06 AM, Kishor Tappita <kishor.tappita at="" gmail.com=""> wrote: > Dear List, > > When trying to find the enriched GO terms using topGO. I get the below > error when trying > to display the significant nodes. The method works fine for MF . I get > an error while computing > enrichment for "BP" > >> showSigOfNodes(GOdata,score(resultKS.elim),firstTerms=5,useInfo="all") > > Error in subGraph(nodesInInducedGraph(dag, startNodes), dag) : > ?invalid arg: snodes contains nodes not in the graph: > GO:0003700, GO:0004984, GO:0005515, GO:0008083, GO:0042803 > >> sessionInfo() > R version 2.9.2 (2009-08-24) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > ?[1] Rgraphviz_1.22.1 ? ? ?hgu133plus2.db_2.2.11 topGO_1.12.0 > ?[4] SparseM_0.80 ? ? ? ? ?graph_1.22.2 ? ? ? ? ?GO.db_2.2.11 > ?[7] RSQLite_0.7-2 ? ? ? ? DBI_0.2-4 ? ? ? ? ? ? AnnotationDbi_1.6.1 > [10] limma_2.18.3 ? ? ? ? ?GEOquery_2.8.0 ? ? ? ?RCurl_0.98-1 > [13] bitops_1.0-4.1 ? ? ? ?Biobase_2.4.1 ? ? ? ? biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] kernlab_0.9-8 ? lattice_0.17-25 tools_2.9.2 ? ? XML_2.5-1 > > Thanks, > kishor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Dear Adrian Thank you so much for the suggestion . I reran the commands with the appropriate compatibility and as usual the application runs superb. Thank you once again. Regards, kishor On Thu, Sep 17, 2009 at 7:09 PM, Adrian Alexa <adrian.alexa at="" gmail.com=""> wrote: > Hi Kishor, > > can it be that the GOdata object and the resultKS.elim are > incompatible? Did you obtain the resultKS.elim object from the GOdata > object? I'm pretty sure that you build the ?resultKS.elim object using > lets say BP ontology and then you build a new GOdata object for MF (or > something similar). Another possibility is that you saved the > resultKS.elim from a previous session and in the current session you > build a topGOdata object which make use of the newly updated GO.db and > then you will of course get a mismatch in the nodes names. > > Hope this helps, > Adrian > > > > > > > > On Thu, Sep 17, 2009 at 11:06 AM, Kishor Tappita > <kishor.tappita at="" gmail.com=""> wrote: >> Dear List, >> >> When trying to find the enriched GO terms using topGO. I get the below >> error when trying >> to display the significant nodes. The method works fine for MF . I get >> an error while computing >> enrichment for "BP" >> >>> showSigOfNodes(GOdata,score(resultKS.elim),firstTerms=5,useInfo="all") >> >> Error in subGraph(nodesInInducedGraph(dag, startNodes), dag) : >> ?invalid arg: snodes contains nodes not in the graph: >> GO:0003700, GO:0004984, GO:0005515, GO:0008083, GO:0042803 >> >>> sessionInfo() >> R version 2.9.2 (2009-08-24) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> [8] base >> >> other attached packages: >> ?[1] Rgraphviz_1.22.1 ? ? ?hgu133plus2.db_2.2.11 topGO_1.12.0 >> ?[4] SparseM_0.80 ? ? ? ? ?graph_1.22.2 ? ? ? ? ?GO.db_2.2.11 >> ?[7] RSQLite_0.7-2 ? ? ? ? DBI_0.2-4 ? ? ? ? ? ? AnnotationDbi_1.6.1 >> [10] limma_2.18.3 ? ? ? ? ?GEOquery_2.8.0 ? ? ? ?RCurl_0.98-1 >> [13] bitops_1.0-4.1 ? ? ? ?Biobase_2.4.1 ? ? ? ? biomaRt_2.0.0 >> >> loaded via a namespace (and not attached): >> [1] kernlab_0.9-8 ? lattice_0.17-25 tools_2.9.2 ? ? XML_2.5-1 >> >> Thanks, >> kishor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
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