I have a data base with gene names and GO annotation for maize. Having selected a gene list, I want to get this annotation file into R in a format that allows me to run GOstat. I am not sure how to proceed. A sample of the annotation file is below. GRMZM2G026396,, GRMZM2G160606,5737,cytoplasm GRMZM2G103702,, GRMZM5G810061,3924,GTPase activity GRMZM5G810061,5525,GTP binding GRMZM2G019356,, GRMZM2G032655,, GRMZM2G098423,51287,NAD binding GRMZM2G136395,, GRMZM2G137676,30599,pectinesterase activity GRMZM2G137676,42545,cell wall modification GRMZM2G137676,5618,cell wall Thanks for any assistance. A pointer to the correct vignette or manual should be enough. Naomi Altman

Hi Naomi, http://bioconductor.org/packages/2.11/bioc/vignettes/GOstats/inst/doc/ GOstatsForUnsupportedOrganisms.pdf Best, Jim On 2/4/2013 10:13 PM, naomi at stat.psu.edu wrote: > I have a data base with gene names and GO annotation for maize. Having > selected a gene list, I want to get this annotation file into R in a > format that allows me to run GOstat. I am not sure how to proceed. A > sample of the annotation file is below. > > GRMZM2G026396,, > GRMZM2G160606,5737,cytoplasm > GRMZM2G103702,, > GRMZM5G810061,3924,GTPase activity > GRMZM5G810061,5525,GTP binding > GRMZM2G019356,, > GRMZM2G032655,, > GRMZM2G098423,51287,NAD binding > GRMZM2G136395,, > GRMZM2G137676,30599,pectinesterase activity > GRMZM2G137676,42545,cell wall modification > GRMZM2G137676,5618,cell wall > > Thanks for any assistance. A pointer to the correct vignette or manual > should be enough. > > Naomi Altman > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099