Hi Marc, I am trying to summarize the GO results for lots of experiments. GOslim was recommended to me as it gives a nice overview. Ideally I would like to have a vector for each experiment, showing a score for each GOslim term which I can then colour/cluster based on over representation I am not exactly sure how the process would works though. Would I do my over representation with all GO terms, and then extract only those that are in GOslim? Or would I have to check all GOterms that make up each GOslim term? Just thinking about it now, if GOslim is a subset of GO terms, I guess it makes most sense to just extract the GOslim terms from my analysis. Cheers, Iain On Thu, Feb 19, 2009 at 11:39 AM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Iain, > > I am a little curious about what you are planning to do with GOSLIM? To > change the annotation used in GOstats, you would normally put the name > of the appropriate annotation package into the annotation slot of the > GOHyperGParams object. But as I am sure you have noticed we don't have > annotation packages for GOSLIM. However, according to the gene ontology > website, a GOSLIM is a subset of the existing GO ontology. So the > appropriate organism package for yeast (which is already based on what > they have at SGD as much as possible) should already provide all the > information you would need for that. > > > Marc > > > > > Iain Wallace wrote: > > Hi all, > > > > I was wondering if somebody could point me in the right direction. I > would > > like to use GOSlim from the SGD > > website< > ftp://genome- ftp.stanford.edu/pub/yeast/data_download/literature_curation/ > >with > > the GOStats package, but I am not sure how to change the > > ontology/annotation. > > > > I am currently using the following set of commands to do my Go analysis. > > library(GOstats) > > library("org.Sc.sgd.db") > > x <- org.Sc.sgdGENENAME #To generate the set of gene names > > mapped_genes <- mappedkeys(x) > > sel<-mapped_genes[1:10] #selected set of genes > > uni<-mapped_genes #universe of genes > > > params=new("GOHyperGParams",geneIds=sel,universeGeneIds=uni,annotati on="org.Sc.sgd.db",ontology="BP",pvalueCutoff=0.05,conditional=FALSE,t estDirection="over") > > over=over=hyperGTest(params) > > > > Thanks for any help, > > > > Iain > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > [[alternative HTML version deleted]]