[R] problems saving and loading (PLMset) objects

[Quin Wills]

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:jmacdon at med.umich.edu] 
Sent: 31 July 2007 14:54
To: Quin Wills
Cc: r-help at 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]]
> 
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-- 
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