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Bosotti, Roberta [Nervianoms]
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@bosotti-roberta-nervianoms-1085
Last seen 10.2 years ago
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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