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[cluste red_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/ [[alternative HTML version deleted]]

Hi Legaie, I am afraid that we don't have annotation support for Streptomyces coelicolor at this time. But I will add this to the list of organisms that we will be adding in the near future. Please send me an email if you think you have information that can help accelerate this process. Marc Legaie, Roxane wrote: > 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[clust ered_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 at warwick.ac.uk > http://www2.warwick.ac.uk/fac/sci/systemsbiology/ > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >

Hi Roxane, I think the problem is due to the 'KEGG.db' annotation package you have assigned to your KEGGHyperGParams 'params'. The assignment should be the annotation package of your microarray platform or an Entrez-based organism one (not sure if one exists for Streptomyces). Also, you didn't supply a sessionInfo() but I would recommend upgrading (if this is not the case) to the latest version of Category and GOstats. To remove the warning messages just make your lists of genes non-redundant with unique() for example. Cheers, J. Legaie, Roxane wrote: > 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[clust ered_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 at warwick.ac.uk > http://www2.warwick.ac.uk/fac/sci/systemsbiology/ > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >