> library(affyPLM)
> data(Dilution)
> pset <- fitPLM(Dilution)
> save(pset, file="tmp.Rdata")
> q()
## restart R
> library(affyPLM)
> load("tmp.Rdata") ## use load() correctly
> class(pset)
[1] "PLMset"
attr(,"package")
[1] "affyPLM"
> erm <- load("tmp.Rdata") ## use load() incorrectly
> class(erm)
[1] "character"
Best,
Jim
Quin Wills wrote:
> 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
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
