[BioC] ExpressionSet, fitPLM confusion

James W. MacDonald jmacdon at med.umich.edu
Thu Dec 14 15:42:00 CET 2006

Hi Georg,

In addition to what Wolfgang told you, the affyPLM package in the devel 
repository won't work with R-2.5.0 yet, because some of the changes that 
have been made to the ExpressionSet object have not been addressed in 
the affyPLM package.

 > dat <- ReadAffy()
 > pset <- fitPLM(dat)
Error in checkSlotAssignment(object, name, value) :
	assignment of an object of class "AnnotatedDataFrame" is not valid for 
slot "phenoData" in an object of class "PLMset"; is(value, "phenoData") 
is not TRUE
In addition: Warning message:
The exprSet class is deprecated, use ExpressionSet instead

Your best bet at this time is to go back to using release versions.



Wolfgang Huber wrote:
> Dear Georg,
> to use the devel versions of Bioconductor (ie what will be Bioconductor
> 2.0) you will need to use a more recent version of R (what will be R
> 2.5): the new code in Biobase uses an argument "msg" of the .Deprecated
> function that was not yet there in R 2.4.
> See http://www.bioconductor.org/download/BioC2.0/
> "BioC 2.0 is currently in development. It is being designed to work with
> R 2.5.z and is expected to be released in April of 2007."
>  Best wishes
>  Wolfgang
>  Otto wrote:
>>Dear Bioconductors,
>>Once more, I am a bit confused about an error linked with the new
>>ExpressionSet class. What I am trying to do is to apply fitPLM to an
>>AffyBatch object. First, I generate the AffyBatch object like this:
>>pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2)
>>Data<-ReadAffy(celfile.path =cel.path, 
>>               filenames = sampleNames(targets),
>>               verbose=TRUE)
>>Then I use fitPLM and get an error:
>>Error in .Deprecated(msg = EXPRSET_DEPR_MSG) : 
>>	unused argument(s) (msg = "The exprSet class is deprecated, use ExpressionSet instead")
>>However ?fitPLM tells me:
>>This function converts an 'AffyBatch' into an 'PLMset' by fitting a
>>specified robust linear model to the probe level data
>>And class() confirms that my object is indeed an AffyBatch:
>>[1] "AffyBatch"
>>[1] "affy"
>>I think I am working with the last versions of the needed libraries
>>(see below). They were updated from the devel repository from
>>source. Any hints?
>>R version 2.4.0 (2006-10-03) 
>>attached base packages:
>>[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    
>>[7] "datasets"  "methods"   "base"     
>>other attached packages:
>>zebrafishcdf      affyPLM        gcrma  matchprobes     affydata         affy 
>>    "1.15.0"     "1.11.8"      "2.7.1"      "1.7.1"     "1.11.1"    "1.13.12" 
>>      affyio      Biobase 
>>     "1.3.1"    "1.13.28"
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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