On Wed, Jan 9, 2013 at 6:36 PM, Fix Ace <acefix at="" rocketmail.com=""> wrote: > > Thank you very much for your reply. > > Does it mean I will have to run: > > bioclite("hgu95av2.db") Yes. If that doesn't work, do this first: source("http://bioconductor.org/biocLite.R") Dan > > I am really new to bioconductor, not quite sure how it runs... > > > ________________________________ > From: James W. MacDonald <jmacdon at="" uw.edu=""> > > Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Sent: Wednesday, January 9, 2013 7:58 AM > Subject: Re: [BioC] topGO quick start guide error > > > > On 1/8/2013 5:31 PM, Fix Ace wrote: >> I just installed topGO and tried to run their example: >> >> when I typed:? >> ? ? ? affyLib<- paste(annotation(ALL), "db", sep = ".") >> ? ? ? affyLib >> ? ? ? [1] "hgu95av2.db" >> ? ? ? ? library(package = affyLib, character.only = TRUE) >> >> got error message: >> ? ? ? Error in library(package = affyLib, character.only = TRUE) : >> ? there is no package called ???hgu95av2.db??? > > That error message tells you what is wrong - you don't have the > hgu95av2.db package installed. > > Best, > > Jim > > >> >> >> Anybody has idea what is going on here? Thanks:) >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> 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 > [[alternative HTML version deleted]] > > > _______________________________________________ > 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

Just realized some typo in the subject of previous post. So would like to raise this question again since nobody answer it last time. This is relevant to usage of GOstat package with unsupported model organism. Thanks. ________________________________ To: "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Wednesday, January 16, 2013 9:38 AM Subject: question about "evidence cole" in data.frame from GOstats packages with unsupported model organisms I am planning to use read.table to create the objects that feed to GOFrame. The manual says that the three columns are required, GO IDs, evidence code and gene IDs. I think I understand the first and third column, but what information should I put in evidence code? For example I have the following in text file: --------------------------------- GO:0002576    ***    gene1 ------------------------------- Does it work? [[alternative HTML version deleted]]