Hello, I was testing over-representation of GO categories and generating nice HTML reports through these commands: >params<-new("GOHyperGParams", >geneIds=genelist1UQ, >universeGeneIds=EntrezUniverse, >annotation="mouse4302", >ontology="BP", >pvalueCutoff=0.001, >conditional=FALSE, >testDirection="over") >GOover<-hyperGTest(params) >htmlReport(GOover, file="GO_MCL_cluster1") However, when i tried to do similar for KEGG pathways and PFAM domains through the following: KEGG: >params<-new("KEGGHyperGParams", >geneIds=genelist1UQ, >universeGeneIds=EntrezUniverse, >annotation="mouse4302", >pvalueCutoff=0.001, >testDirection="over") >keggOver<-hyperGTest(params) >htmlReport(keggOver, file="GO_MCL_cluster1") PFAM: >params<-new("PFAMHyperGParams", >geneIds=genelist1UQ, >universeGeneIds=EntrezUniverse, >annotation="mouse4302", >pvalueCutoff=0.001, >testDirection="over") >pfamOver<-hyperGTest(params) >htmlReport(pfamOver, file="GO_MCL_cluster1") -the "problem" with these reports is: 1)unlike in GO report there is no "Term" column which human can understand, and only KEGG/PFAM ids are listed 2)to make things worse - there is no html links from these ids, and to see what are the things i have to paste them individually into the google etc. So is there an easy way to add links to the descriptive column to the HTML reports and to add HTML links to them? Thanks a lot! Sergei -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Hi Siarhei, Siarhei Manakou <sm7 at="" sanger.ac.uk=""> writes: > However, when i tried to do similar for KEGG pathways and PFAM domains > through the following: [snip] > -the "problem" with these reports is: > 1)unlike in GO report there is no "Term" column which human can > understand, and only KEGG/PFAM ids are listed This should easy to add for KEGG since we have a KEGG annotation package that maps KEGG ids to names. I'm not sure yet about PFAM since I don't know if we have an annotation source within BioC that maps PFAM ids to more meaningful names. > 2)to make things worse - there is no html links from these ids, and to > see what are the things i have to paste them individually into the > google etc. This is also possible. > So is there an easy way to add links to the descriptive column to the > HTML reports and to add HTML links to them? Depends on your definition of easy. The coding task should not be too difficult and what is done for GO can be used as a template. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/