[BioC] error with display of significant nodes using topGO

[Adrian Alexa]

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
>
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