Dear all,
I am currently working on Streptomyces coelicolor microarray data.
I have some clusters of genes and I would like to use the Kegg.db package with GOstats to obtain a pathway annotation.

Here my code (and error messages!):
> clustered_entrezgenes = read.table("Clustered_EntrezGenes.txt",header=TRUE,sep="\t")
> all_ids = as.character(clustered_entrezgenes$EntrezGenes[])   #all Entrez ids in my clustering
> cluster1_ids = as.character(clustered_entrezgenes$EntrezGenes[clustered_entrezgenes$Cluster==1])  # Entrez ids in cluster number 1
> hgCutoff <- 0.01
> params <- new("KEGGHyperGParams", geneIds = cluster1_ids, universeGeneIds = all_ids, annotation = "KEGG.db",  pvalueCutoff= hgCutoff,testDirection = "over")
Warning messages:
1: In makeValidParams(.Object) : removing duplicate IDs in geneIds
2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds
> 
> over_kegg<- hyperGTest(params)
Error in get(paste(lib, name, sep = "")) : 
  variable "KEGGPATH" was not found
Error in as.list(getDataEnv("PATH", annotation(p))) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.list'
> 

Can you help me to find out the problem?
Thank you very much.
Roxane


Roxane LEGAIE
Bioinformatician
--
Warwick Systems Biology Centre
Coventry House
University of Warwick
Coventry CV4 7AL
U.K.
+44 (0)24 761 50332
R.Legaie@warwick.ac.uk
http://www2.warwick.ac.uk/fac/sci/systemsbiology/


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