Hello, When doing this: > params <- new( > "GOHyperGParams", > geneIds=ipilist, > universeGeneIds=names(as.list(get(paste(annotation,"GO",sep="")))), > annotation=annotation, > ontology="BP", > pvalueCutoff=0.001, > conditional=FALSE, > testDirection = "over" > ) > hgOver <- hyperGTest(params) with 'ipilist' being a vector of IPI ids, and 'annotation' being a AnnBuilder package I build to map go terms to IPI ids via EntrezIDs, I get the following error: > Error in getUniverseHelper(probes, lib, entrezIds) : > No Entrez Gene ids left in universe The 'universe' construct is supposed to return all IPI ids from the annotation package. Please enlighten me as to where I err! Something else: "GOHyperGParams" is not well documented on my system: > ?GOHyperGParams-class gets me this: > Error in eval(expr, envir, enclos) : object "GOHyperGParams" not found > Error in .helpForCall(e1Expr, parent.frame()) : > error in trying to evaluate the expression for argument 'e1' > (GOHyperGParams) My specific questions are: - is there an option like "ontology='all'"? - is there an option like "testDirection='both'"? Thanks for any hints, Joh

Hi, Johannes Graumann <johannes_graumann at="" web.de=""> writes: >> params <- new( >> "GOHyperGParams", >> geneIds=ipilist, >> universeGeneIds=names(as.list(get(paste(annotation,"GO",sep="")))), >> annotation=annotation, >> ontology="BP", >> pvalueCutoff=0.001, >> conditional=FALSE, >> testDirection = "over" >> ) >> hgOver <- hyperGTest(params) > > with 'ipilist' being a vector of IPI ids, and 'annotation' being a > AnnBuilder package I build to map go terms to IPI ids via EntrezIDs, > I get the following error: > >> Error in getUniverseHelper(probes, lib, entrezIds) : >> No Entrez Gene ids left in universe > > The 'universe' construct is supposed to return all IPI ids from the > annotation package. > > Please enlighten me as to where I err! The environments from the annotation data packages that get used for the calculation are hard-coded. Except when using the YEAST package, the geneIds should be Entrez Gene IDs or at least be the same as what is in the yourpkgENTREZID environment. It isn't clear to me what you have and your your IPI IDs are. > Something else: "GOHyperGParams" is not well documented on my system: > >> ?GOHyperGParams-class Please try: ?"GOHyperGParams-class" or class ? GOHyperGParams > My specific questions are: > - is there an option like "ontology='all'"? There is not currently such an option. You have to test each ontology seprately. I believe that the current approach is more conservative. The universe of Entrez IDs is reduced to those that have at least one annotation in the specified GO ontology. If one tested all ontologies together, the universe would grow and, in general, you would get smaller p-values for the same gene list. > - is there an option like "testDirection='both'"? Sorry, no. Are you thinking about something that is combined? Computing both results isn't difficult: pUnder <- pOver testDirection(pUnder) <- "under" ansOver = hyperGTest(pOver) ansUnder = hyperGTest(pUnder) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org