Hi, The mapping functions like match and  %in% or overlapping functions in range data could help. Otherwise, a simple script in python could be faster. John ________________________________ From: Laurent Pays [guest] To: bioconductor@r-project.org; Laurent.Pays@univ-lyon1.fr Sent: Monday, September 17, 2012 11:15 AM Subject: [BioC] How to filter a list of genes by their ontology Hi, After analysing my arrays for differentially expressed genes, I get a list of genes Id. To reduce even more the number of genes in this list, I would like to retain only genes related to the immune system. I've looked for packages dealing with "ontology" but I couldn't find any doing this simple task... Any idea on what package/function I could use? Thanks in advance for your help. L.P -- output of sessionInfo(): R version 2.7.0 (2008-04-22) powerpc-apple-darwin8.10.1 locale: fr_FR.UTF-8/fr_FR.UTF-8/C/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] stats    graphics  grDevices utils    datasets  methods  base  -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]