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 >> >