Hi I would like to do some post annotation analysis on my gene list from an Affy experiment. Basically we want to see if the set of genes has any statistically over represented GO ids in comparison to the total of the genes in the chip. An over representation probability should be given to each of the categories. This is in line with what some packages already do: EASE, GeneMerge, GOminer, fatiGO (web)... But I was wondering if somebody did something like this already in Bioconductor or maybe it is not a good idea to implement this in R as it is not the fastest text searcher. Any suggestions welcomed Thanks! Jose -- Jose Duarte MRC Functional Genetics Unit Department of Human Anatomy and Genetics University of Oxford South Parks Road Oxford OX1 3QX Phone: +44 (0)1865 282650 e-mail: jose.duarte@anat.ox.ac.uk

Jose, Assuming that you have an annotation data package built for your data and the GO data package (from Bioconductor), you can use a combination of lookups from GO to get terms of interest and then use lookup of those terms to see if any of your probes are annotated with them (see ?lookUp and ?getGO and the package annotate). Doing the latter on subsets of your data and the whole data set should allow you to form the EASE score (or fisher exact test, etc.). However, know that the annotation packages use locuslink information and the other programs may use other (with respect to GO) and perhaps more complete information and that the answers that you get from the other programs will likely be slightly different. Sean -- Sean Davis, M.D., Ph.D. Clinical Fellow National Institutes of Health National Cancer Institute National Human Genome Research Institute Clinical Fellow, Johns Hopkins Department of Pediatric Oncology -- On 12/12/03 12:36 PM, "Jose Duarte" <jose.duarte@human- anatomy.oxford.ac.uk=""> wrote: > Hi > > I would like to do some post annotation analysis on my gene list from an > Affy experiment. Basically we want to see if the set of genes has any > statistically over represented GO ids in comparison to the total of the > genes in the chip. An over representation probability should be given to > each of the categories. > > This is in line with what some packages already do: EASE, GeneMerge, > GOminer, fatiGO (web)... But I was wondering if somebody did something > like this already in Bioconductor or maybe it is not a good idea to > implement this in R as it is not the fastest text searcher. > > Any suggestions welcomed > > > Thanks! > > Jose > > > > >

Hi Try onto-express. I like it quite a lot. Intelligent Systems and Bioinformatics Laboratory http://vortex.cs.wayne.edu/research.htm Yours, Lawrence ______________________________ Lawrence Paul Petalidis Ph.D. Candidate University of Cambridge Department of Pathology ______________________________ -----Original Message----- From: bioconductor-bounces+lpp22=cam.ac.uk@stat.math.ethz.ch [mailto:bioconductor-bounces+lpp22=cam.ac.uk@stat.math.ethz.ch]On Behalf Of Jose Duarte Sent: 12 December 2003 17:37 To: bioconductor@stat.math.ethz.ch Subject: [BioC] GO analysis Hi I would like to do some post annotation analysis on my gene list from an Affy experiment. Basically we want to see if the set of genes has any statistically over represented GO ids in comparison to the total of the genes in the chip. An over representation probability should be given to each of the categories. This is in line with what some packages already do: EASE, GeneMerge, GOminer, fatiGO (web)... But I was wondering if somebody did something like this already in Bioconductor or maybe it is not a good idea to implement this in R as it is not the fastest text searcher. Any suggestions welcomed Thanks! Jose -- Jose Duarte MRC Functional Genetics Unit Department of Human Anatomy and Genetics University of Oxford South Parks Road Oxford OX1 3QX Phone: +44 (0)1865 282650 e-mail: jose.duarte@anat.ox.ac.uk _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Dear Jose, You might want to look at our tool http://fatigo.bioinfo.cnio.es/ (The paper describing it is in press at Bioinformatics). It should start working directly with Affy in a week or so. For now, you would neet to go to EnsMart, input your list of affy ids, then output the ensemble gene names, and input that to fatigo. Best, R. On Friday 12 December 2003 18:36, Jose Duarte wrote: > Hi > > I would like to do some post annotation analysis on my gene list from an > Affy experiment. Basically we want to see if the set of genes has any > statistically over represented GO ids in comparison to the total of the > genes in the chip. An over representation probability should be given to > each of the categories. > > This is in line with what some packages already do: EASE, GeneMerge, > GOminer, fatiGO (web)... But I was wondering if somebody did something > like this already in Bioconductor or maybe it is not a good idea to > implement this in R as it is not the fastest text searcher. > > Any suggestions welcomed > > > Thanks! > > Jose -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz PGP KeyID: 0xE89B3462 (http://bioinfo.cnio.es/~rdiaz/0xE89B3462.asc)