thanks James, I though that the identifiers with wich you succeeded were the systematic names....for me common names were the other ones NOT belonging with Y. Best, Maria Maria Persico, PhD. student http://cbm.bio.uniroma2.it/~maria/ MINT database group Universita' di Tor Vergata, via della Ricerca scientifica 11 00133 Roma, Italy Tel +39 0672594315 (Supervisor's room) Fax +39 0672594766 Mobile phone: +393479715662 e-mail maria at cbm.bio.uniroma2.it On Tue, 4 Jul 2006, James W. MacDonald wrote: > Hi Maria, > > maria at cbm.bio.uniroma2.it wrote: >> Hello everyone, >> >> I'm trying to calculate the probability that 2 YEAST proteins share the >> same biological process by chance as suggested in the Liu's paper (PMID >> 15905281); I want a p-value associated to each protein pair in my data >> set; I would like to use the Bioconductor implementation of GO analysis: >> in the help page of the GOHyperG I read the following phrase: >> >> " For S. cerevisiae if the 'lib' argument is set to '"YEAST"' then >> comparisons and statistics are computed using common names and are with >> respect to all genes annotated in the S. cerevisiae genome not with >> respect to any microarray chip." >> >> this is exactly my case, I don't have a chip. I load the libraries GOstats >> and YEAST and I choose two common names of two proteins to see if the >> pipeline works: >> >> > library(GOstats) >> > library(YEAST) >> >> >> > myYCM<-c("RAD24","DMC1") >> >> >> At this point I got the following error message: >> >> >> > xx<-GOHyperG(myYCM, lib="YEAST", what="BP", universe=NULL) >> >> Error in length(p at universeGeneIds) - numAtCat : >> non-numeric argument to binary operator >> >> I suppose that the problem is the universe; what should I provide as >> universe value if comparisons and statistics are computed using common >> names....in the error message I see p at universeGeneIds!? > > I don't think that is the problem. I think the common names expected are > things like "YPL113C" "YNL055C" "YKL154W" "YNR076W" (I believe these > are the Locus Tags?). If I look up the correct locus tags for your genes, > things work for me. > >> myYCM<-c("YER173W", "YER179W") >> xx<-GOHyperG(myYCM, lib="YEAST", what="BP", universe=NULL) >> > > HTH, > > Jim > > >> >> thanks, >> >> Maria >> >> Maria Persico, PhD. student >> http://cbm.bio.uniroma2.it/~maria/ >> MINT database group >> Universita' di Tor Vergata, via della Ricerca scientifica 11 >> 00133 Roma, Italy >> Tel +39 0672594315 (Supervisor's room) >> Fax +39 0672594766 >> Mobile phone: +393479715662 >> e-mail maria at cbm.bio.uniroma2.it >> >> _______________________________________________ >> 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 > University of Michigan > Affymetrix and cDNA Microarray Core > 1500 E Medical Center Drive > Ann Arbor MI 48109 > 734-647-5623 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues. >