Dear Eichinger, I would think topGO must do the job: http://www.bioconductor.org/help/bioc-views/2.8/bioc/html/topGO.html Yours, Thao On Thu, Feb 24, 2011 at 9:18 AM, Ludwig Eichinger < ludwig.eichinger@uni-koeln.de> wrote: > Dear colleagues, > > we would like to analyse gene ontology term enrichment for a RNAseq > experiment of human cells. Can we do this with bioconductor (which R > version do we need) and if yes, how can we do it? > > Thank you very much for your advice. > > Best regards > > Ludwig Eichinger > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Prof. Dr. Ludwig Eichinger > Centre for Biochemistry > Medical Faculty > University of Cologne > Joseph-Stelzmann-Str. 52 > D-50931 Koeln > > Tel. 0049-221-4786928 > FAX 0049-221-4786979 > > Dictyostelium Genome Project and Fuctional Analysis: > http://www.uni-koeln.de/med-fak/biochemie/transcriptomics/ > http://www.uni-koeln.de/dictyostelium/ > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > _______________________________________________ > 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]]

Hi Ludwig The goseq package is designed for this purpose. http://bioconductor.org/help/bioc-views/2.7/bioc/html/goseq.html Cheers Davis On Feb 24, 2011, at 7:18 PM, Ludwig Eichinger wrote: > Dear colleagues, > > we would like to analyse gene ontology term enrichment for a RNAseq > experiment of human cells. Can we do this with bioconductor (which R > version do we need) and if yes, how can we do it? > > Thank you very much for your advice. > > Best regards > > Ludwig Eichinger > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Prof. Dr. Ludwig Eichinger > Centre for Biochemistry > Medical Faculty > University of Cologne > Joseph-Stelzmann-Str. 52 > D-50931 Koeln > > Tel. 0049-221-4786928 > FAX 0049-221-4786979 > > Dictyostelium Genome Project and Fuctional Analysis: > http://www.uni-koeln.de/med-fak/biochemie/transcriptomics/ > http://www.uni-koeln.de/dictyostelium/ > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- -- Davis J McCarthy Research Technician Bioinformatics Division Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville, Vic 3052, Australia dmccarthy at wehi.edu.au http://www.wehi.edu.au ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}