[BioC] makeGOGraph error

[Wolfgang Huber]

Hi Roberta,

I had a similar problem recently, and it turned out to be a matter of 
versioning between the GOstats package and GO package. There have been 
some changes in the way data is presented in the GO package, which 
required a tiny but important modification in makeGOGraph. Make sure to 
use the most recent versions of both, and let me know if that helps.

For me it works with
GO 1.6.8
GOstats 1.1.2

    Best wishes
     Wolfgang

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

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber