Erm, Jim I am loading in the affyPLM package first (when needed) and this was a question based on loading/saving R objects. PLMset was an example.
Many thanks, Quin -----Original Message----- From: James W. MacDonald [mailto:[EMAIL PROTECTED] Sent: 31 July 2007 14:54 To: Quin Wills Cc: r-help@stat.math.ethz.ch Subject: Re: [R] problems saving and loading (PLMset) objects Hi Quin, First off, you should ask questions about Bioconductor packages on the BioC listserv rather than R-help. Anyway, I don't think your PLMset objects are coming out all wrong - it doesn't appear that you are loading the affyPLM package first, which is required for R to know anything about the PLMset object (this object is defined in affyPLM, so without the package R has no idea what it is). Best, Jim Quin Wills wrote: > Hi > > > > I'm running the latest R on a presumably up to date Linux server. > > > > 'Doing something silly I'm sure, but can't see why my saved PLMset objects > come out all wrong. To use an example: > > > > Setting up an example PLMset (I have the same problem no matter what example > I use) > >> library(affyPLM) > >> data(Dilution) # affybatch object > >> Dilution = updateObject(Dilution) > >> options(width=36) > >> expr <- fitPLM(Dilution) > > > > > > This works, and I'm able to get the probeset coefficients with coefs(expr). > until I save and try reloading: > >> save(expr, file="expr.RData") > >> rm(expr) # just to be sure > >> expr <- load(expr.RData) > > > > > > Now, running coefs(expr) says: > >> Error in function (classes, fdef, mtable) : unable to find an inherited > method for function "coefs", for signature "character" > > > > > > Trying str(exp) just gives the following: > >> chr "exp" > > > > expr.Rdata appears to save properly (in that there is an actual file with > notable size in my working directory). > > > > Thanks in advance, > > Quin > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.