Hi, I am new to GO analysis. What I want to do is pretty simple: I have a list of mouse gene (gene symbol as ID) from illumina expression experiment and I want to found out if any GO term is significantly enriched among these genes. It seems GOstats and topGO are all designed for Affymetrix data. I guess I could (in theory) use GO.db to query GO,but I am afraid of reinventing things. Any suggestions? Thanks! Yupu

Hi Yupu, You should read the tutorial vignette for the GOstats package. I think it will probably show you what you need to know: You can find the GOstats package here: http://www.bioconductor.org/packages/release/bioc/html/GOstats.html And the tutorial here: http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/in st/doc/GOstatsHyperG.pdf Marc Yupu Liang wrote: > Hi, > > I am new to GO analysis. > > What I want to do is pretty simple: I have a list of mouse gene (gene > symbol as ID) from illumina expression experiment and I want to found > out if any GO term is significantly enriched among these genes. > > It seems GOstats and topGO are all designed for Affymetrix data. > > I guess I could (in theory) use GO.db to query GO,but I am afraid of > reinventing things. > > Any suggestions? > > Thanks! > Yupu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi, Yopu, I am afraid that is not true. GOstats is not only designed for Affymetrix, but also for other platforms (of course, including illumina). As long as you have the annotation database, which would allow you mapping the nuIDs (or illumina's manufacture IDs) onto EntrezIDs, you should be able to use GOstats. Yupu Liang wrote: > Hi, > > I am new to GO analysis. > > What I want to do is pretty simple: I have a list of mouse gene (gene > symbol as ID) from illumina expression experiment and I want to found > out if any GO term is significantly enriched among these genes. > > It seems GOstats and topGO are all designed for Affymetrix data. > > I guess I could (in theory) use GO.db to query GO,but I am afraid of > reinventing things. > > Any suggestions? > > Thanks! > Yupu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org

Hi Yupu, Lets keep this message on list so that others can benefit from our discussion. The annotation parameter is where you need to specify the annotation package that you are going to use. You can install the appropriate annotation package using biocLite(). Most major platforms are supported and the annotation package is traditionally named after the platform that it is based on. You can peruse our list of "stock" annotation packages here: http://www.bioconductor.org/packages/release/data/annotation/ Please let us know if the platform you are looking for is not there. In that case, we have also provided a way for you to make your own. You can find details on that in the SQLForge vignette in the AnnotationDbi package: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.h tml Marc Yupu Liang wrote: > Marc: > > Hi, thanks for the response and I have read the docs but I got > confused/lost at > > > params <- new("GOHyperGParams", geneIds = selectedEntrezIds, > + universeGeneIds = entrezUniverse, annotation = "hgu95av2.db", > + ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE, > + testDirection = "over") > > I am not sure what I should use for the annotation parameter > > And from the class description of GOHyperGParams-class, it says > > annotation:A string giving the name of the annotation data package for > the chip used to generate the data. > > Yupu > > > On Sep 16, 2009, at 5:51 PM, Marc Carlson wrote: > >> Hi Yupu, >> >> You should read the tutorial vignette for the GOstats package. I think >> it will probably show you what you need to know: >> >> You can find the GOstats package here: >> >> http://www.bioconductor.org/packages/release/bioc/html/GOstats.html >> >> And the tutorial here: >> >> http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats /inst/doc/GOstatsHyperG.pdf >> >> >> >> >> Marc >> >> >> >> >> >> Yupu Liang wrote: >>> Hi, >>> >>> I am new to GO analysis. >>> >>> What I want to do is pretty simple: I have a list of mouse gene (gene >>> symbol as ID) from illumina expression experiment and I want to found >>> out if any GO term is significantly enriched among these genes. >>> >>> It seems GOstats and topGO are all designed for Affymetrix data. >>> >>> I guess I could (in theory) use GO.db to query GO,but I am afraid of >>> reinventing things. >>> >>> Any suggestions? >>> >>> Thanks! >>> Yupu >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > >

Hi Yupu, you can use topGO package with any list of genes as long as you have the gene-to-GO mapping. You can use either Bioconductor annotation packages or pain text files which list the gene-to-GO mapping. Look at the manual page for "annFun" function in topGO for more information. Best, Adrian On Wed, Sep 16, 2009 at 11:26 PM, Yupu Liang <liang at="" cbio.mskcc.org=""> wrote: > Hi, > > I am new to GO analysis. > > What I want to do is pretty simple: I have a list of mouse gene (gene symbol > as ID) from illumina expression experiment and I want to found out if any GO > term is significantly enriched among these genes. > > It seems GOstats and topGO are all designed for Affymetrix data. > > I guess I could (in theory) use GO.db to query GO,but I am afraid of > reinventing things. > > Any suggestions? > > Thanks! > Yupu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >