Hi Alex, Alex Tsoi wrote: > Thanks for the information, but I guess GOHyperG does not output the Gene > ontology term, while hyperGTest output both the GOid, as well as the GO > term. However, my another question is how could I retrieve information about > the genes that have the enriched gene ontology (ie. which genes are > annotated with the enriched gene ontology)? > There is a function in affycoretools (hyperGoutput()) that does pretty much what I think you want to do. Best, Jim > The hyperGTest gives us information about the count of the differentially > expressed genes that are annotated with that enriched gene ontology, and it > also gives the count of the genes in the array that are annotated with the > GO, but I would like to have information about which differentially > expressed genes are annotated with those GO. So I guess my question is given > a set of Locus link ID, is it possible to find the gene ontologies > associated with them by using the array's package : hgu133plus2 ? > > (I tried to use GOLOCUSID2GO to find all the ontologies associated with each > of the differentially expressed genes, and see if each of the ontology is > enriched by looking back the result of the hyperGTest, but I found the > results are not coherent; ie. the GO annotations of the package hgu133plus2 > is not coherent with the result of the GOLOCUSID2GO ) > > So that's why I would like to retrieve the GO ids from a set of locus link > ids. > > Appreciate for any help or comment > > > > On 7/23/07, Seth Falcon <sfalcon at="" fhcrc.org=""> wrote: > >> "Alex Tsoi" <tsoi.teen at="" gmail.com=""> writes: >> >> >>> Dear all, >>> >>> I am using GOHyperG to get the onverrepresented gene ontology of a set >>> >> of >> >>> genes, and the results give the gene ontology IDs, I just wondering if I >>> could also get the gene ontology terms in the results ; >>> >> What do you mean by terms? Does the summary method on the test result >> do what you want? Try: >> >> ans <- hyperGTest(yourParams) >> summary(ans) >> >> >>> and also, could someone shows me how I could get the gene ontology >>> terms from a set of gene ontology IDs ? >>> >> Perhaps you want: >> >> library("GO") >> someGOTerms <- mget(someGOIDs, GOTERM) >> >> Have you had a look at the vignette that comes with GOstats? Try: >> >> library("GOstats") >> openVignette(package="GOstats") >> >> >> + seth >> >> -- >> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research >> Center >> http://bioconductor.org >> >> > > > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623