[BioC] makeGOGraph error

[Bosotti, Roberta [Nervianoms]]

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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