[BioC] error with display of significant nodes using topGO

Kishor Tappita kishor.tappita at gmail.com
Thu Sep 17 11:06:12 CEST 2009

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)

LC_COLLATE=English_United States.1252;LC_CTYPE=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


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