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 inheritedmethod 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]]
you just need to say:
load("expr.RData")
You should not be assigning it to 'expr' since it is already
'load'ed
On 7/30/07, Quin Wills <wills at stats.ox.ac.uk>
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 at 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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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 at 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