Roberta, Ah, R-1.9.1 is the issue, I believe. Bioconductor release 1.5 requires at least R-2.0.0, if I'm not mistaken. You can still get bioconductor 1.4 release here (http://www.bioconductor.org/repository/release1.4/package/html/ index.html), but I think it would probably be best to upgrade to R-2.0.1 as the ultimate solution. Sean On Jan 25, 2005, at 12:52 PM, Bosotti, Roberta [Nervianoms] wrote: > Hi Sean, > > thanks for your reply. I downloaded it from Bioconductor site, I guess > it is > the latest one. What I realized meanwhile is taht the GOstats package > gives > me error messages on the GO and hgu95av2 versions: > >> require(GOstats) > Loading required package: GOstats > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: annotate > Loading required package: RBGL > Loading required package: genefilter > Loading required package: multtest > [1] TRUE > Warning messages: > 1: Your version of hgu95av2 must be at least 1.6.x in: f(libname, > pkgname) > 2: You must have package GO version >= 1.6.0 in: f(libname, pkgname) > > Regarding GO, I have 1.5.0 version, so that's why. I upgraded to > version > 1.6.8, but this is not supported by my R version (R1.9.1). Do you know > where > I can find GO version 1.6.0? Or where I can download a newer version > of R > for Unix? > Regarding Affy annotation file, I'd actually work with the 133plus, so > I > suspect that the package do not support the 133plus version (in the > release > notes it is suggested the usage of hug95av2). Did it sounds correct to > you? > > Thanks again > > Roberta > > -----Original Message----- > From: Sean Davis [mailto:sdavis2@mail.nih.gov] > Sent: Tuesday, January 25, 2005 5:01 PM > To: Bosotti, Roberta [Nervianoms] > Cc: 'bioconductor@stat.math.ethz.ch' > Subject: Re: [BioC] Problem with GOHyperG > > > Roberta, > > My guess is that you are using an older version of GOHyperG. Install a > newer version will likely help. > > Sean > > On Jan 25, 2005, at 10:23 AM, Bosotti, Roberta [Nervianoms] wrote: > >> Hi List, >> >> I'm using GOHyperG to calculate pval in hyper geometric test, but I >> got an >> error message. >> >> Here are the commands I typed: >> >> require(hgu133plus2) >> require(GO) >> require(graph) >> require(GOstats) >> require(annotate) >> my.go<-"BP" >> gGhyp <- GOHyperG(gNsLL, lib="hgu133plus2", what=my.go) >> >> #where gNsLL is a list of LocusLink. >> >> And here is the error message I got: >> >> Error in match.fun(FUN) : Object "Ontology" not found >> >> Can anybody help me in understanding what I'm doing wrong? >> >> Thanks, >> >> Roberta >> >> Roberta Bosotti >> Biology Dep., Genomics Unit >> Nerviano Medical Science s.r.l. >> viale Pasteur 10, >> 20014 Nerviano (MI) - Italy >> roberta.bosotti@nervianoms.com >> >> >> >> >> >> >> >> >> >> ********************************************************************** >> * >> ***** >> *** >> DISCLAIMER AND CONFIDENTIAL NOTICE\ \ The information >> contai...{{dropped}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > ******************************************************************** *** > ***** > *** > DISCLAIMER AND CONFIDENTIAL NOTICE > > The information contained in this message and any attachment thereto > is to be considered privileged and confidential and is intended for the > addressee(s) designated. All rights related to the message itself and > its attachments are reserved. If you are not the addressee, any > disclosure, reproduction, distribution, on-transmission or use of this > communication are strictly prohibited. If you have received this > transmission in error, please notify us immediately by return email > or telephone and destroy the original message. > > Le informazioni contenute nel presente messaggio e nei suoi allegati > devono essere considerate strettamente confidenziali e riservate > esclusivamente ai destinatari indicati. Sono riservati tutti i diritti > relativi al messaggio e ai suoi allegati. La lettura, la riproduzione, > la diffusione, la ritrasmissione di tutto quanto contenuto nel presente > messaggio ? consentita esclusivamente ai soggetti destinatari. > Se non doveste essere tra i destinatari indicati, > ovvero qualora abbiate ricevuto per errore questo messaggio > Vi preghiamo di darcene comunicazione e di rimuovere il messaggio > stesso e gli allegati dal Vostro sistema.