[BioC] error with display of significant nodes using topGO

[Kishor Tappita]

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
>>
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>