[BioC] KEGG.db in GoStats with Streptomyces coelicolor

[Marc Carlson]

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[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 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
>
>