Dear all, I would like to know if there is a way to use the hyperGTest function in the Category package if I don?t have an annotation package. I have the ensembl id?s of the genes in my microarray as well as all the GO terms associated with them. If there is other tool that does the same job without the need of specifying the annotation package I will also be glad the hear about. Best regards, Jo?o Fadista

You might try the topGO package. Best, Jim Jo?o Fadista wrote: > Dear all, > > I would like to know if there is a way to use the hyperGTest function in the Category package if I don?t have an annotation package. I have the ensembl id?s of the genes in my microarray as well as all the GO terms associated with them. > > If there is other tool that does the same job without the need of specifying the annotation package I will also be glad the hear about. > > > Best regards, > Jo?o Fadista > > _______________________________________________ > 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 -- 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

Hi, Sorry for the delay in responding. In a sense, you now always have a package, at least for organisms where there is a annotation package of the form org.Hs.eg.db, in your case you have two issues you need to deal with 1) a map from Ensembl to EntrezGene (since that is the basis for that package). At some time, during this release cycle Ensembl ids are going to be added to that package so that you won't even need to do that soon. 2) you need to decide what your universe is, and that is a problem typically, since it should reflect the genes you assayed, or could have detected. Selecting this has an enormous effect on p-values so you should exercise some caution. params = new("GOHyperGParams", geneIds=myGenes, universeGeneIds=myUniverse, annotation="org.Hs.eg.db", ontology="BP", pvalueCutoff=0.01, conditional=FALSE, testDirection="over") hgOver = hyperGTest(params) which suitable choices for myGenes and myUniverse, should do what you want. best wishes Robert Jo?o Fadista wrote: > Dear all, > > I would like to know if there is a way to use the hyperGTest function in the Category package if I don?t have an annotation package. I have the ensembl id?s of the genes in my microarray as well as all the GO terms associated with them. > > If there is other tool that does the same job without the need of specifying the annotation package I will also be glad the hear about. > > > Best regards, > Jo?o Fadista > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org