Dear Sean, thanks for your reply. is there a vignette/examples for using GOStats output data in Rgraphviz. may be i am using wrong key words in searching google. I found one link in bioconductor that points to a dead link (http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/r graphviz/) Thanks srini --- Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Jan 4, 2008 10:56 AM, Srinivas Iyyer > <srini_iyyer_bio at="" yahoo.com=""> wrote: > > > Dear Group, > > I used hyperGTest using 'conditional' parameter as > > 'True'. > > > > I generated HTML report of all enriched terms. > There > > are many such HTML tables that are difficult to > look > > at and reason biologically. > > > > Are (IS) there any methods (more than one) to > > represent enriched terms, their P-values > graphically. > > > > Such as drawing GO tree and color enriched term > nodes > > OR a heatmap? > > > > If so, could you please let me know modules that > can > > help me in this task. > > > > Hi, Srini. You might look at Rgraphviz. > > Sean > ________________________________________________________________ ____________________ Never miss a thing. Make Yahoo your home page.

Dear Group, I did hyperGTest in GOStats package and trying to plot the enriched terms onto GO tree. >gp <- new("GOHyperGParams", geneIds = upids, universeGeneIds = euniv, ontology = "BP", annotation = "rgug4130a", pvalueCutoff = hgCutoff, conditional = TRUE, testDirection = "over") >hgO <- hyperGTest(gp) >treedat <- GOGraph(summary(hgO)$GOBPID,GOBPPARENTS) >pdf ("bpCutLeavestreeTest.pdf", width=100, height = 100,paper="special") > plot(treedat) Error in as.double(y) : cannot coerce to vector Could I get some help in this error. what is wrong here? thanks Srini --- Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Jan 4, 2008 10:56 AM, Srinivas Iyyer > <srini_iyyer_bio at="" yahoo.com=""> wrote: > > > Dear Group, > > I used hyperGTest using 'conditional' parameter as > > 'True'. > > > > I generated HTML report of all enriched terms. > There > > are many such HTML tables that are difficult to > look > > at and reason biologically. > > > > Are (IS) there any methods (more than one) to > > represent enriched terms, their P-values > graphically. > > > > Such as drawing GO tree and color enriched term > nodes > > OR a heatmap? > > > > If so, could you please let me know modules that > can > > help me in this task. > > > > Hi, Srini. You might look at Rgraphviz. > > Sean > ________________________________________________________________ ____________________ Never miss a thing. Make Yahoo your home page.