[BioC] makeGOGraph error

[Robert Gentleman]

On Feb 14, 2005, at 12:26 AM, Bosotti, Roberta [Nervianoms] wrote:

> Dear list,
>
> sorry to bother you, but I'm experiencing some problem in using GOstats
> package. I'm trying to find the enrichment in GO family of a set of  
> genes
> for which I have the LocusLink ID in a txt file.
> When I reach the point of using makeGOGraph I encounter this error  
> message:
>
> Error in clearNode(node, object) : NA is not a node in the graph
>
> I'm using R 2.0.1 and bioconductor 1.5
> Here is the script I'm running:
>
>> require(GO)
> Loading required package: GO
> [1] TRUE
>> require(graph)
> Loading required package: graph
> Loading required package: cluster
> Loading required package: Ruuid
> Creating a new generic function for "print" in "Ruuid"
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>          Vignettes contain introductory material.  To view,
>          simply type: openVignette()
>          For details on reading vignettes, see
>          the openVignette help page.
> [1] TRUE
>> require(GOstats)
> Loading required package: GOstats
> Loading required package: annotate
> Loading required package: RBGL
> Loading required package: xtable
>
> Attaching package 'xtable':
>
>
>         The following object(s) are masked from package:graph :
>
>          label
>
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Loading required package: multtest
> Loading required package: reposTools
>
> Loading required package: hgu95av2
> [1] TRUE
>> require(annotate)
> [1] TRUE
>> gNsel<-geneNames(diffexpr.iqr.rma) # diffexpr.iqr.rma is a txt file  
>> with a
> list of LocusLink IDs
>> my.go<-"BP"
>>  p.value<-0.01
>> gNsLL <- as.character(unique(unlist(mget(gNsel,  
>> env=hgu133plus2LOCUSID,
> ifnotfound=NA))))

You might want to remove the NA's in gNsLL at this point.

>> gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go)
>> gGO <- makeGOGraph(gNsLL, my.go)

   What version of GO and of GOstats are you using(please try to report  
version numbers for R and packages when reporting errors)?

  If they are the most recent, then we might need to have a copy of  
gNsLL in order to track down the problem.

  Robert


> Error in clearNode(node, object) : NA is not a node in the graph
>
> Have anybody encountered a similar problem?
>
> Thanks, Roberta
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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