[BioC] ExpressionSet, fitPLM confusion

[Wolfgang Huber]

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:
> 
> targets<-new("AnnotatedDataFrame")
> 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:
> 
> Pset<-fitPLM(Data)
> 
> 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:
> 
> class(Data)
> [1] "AffyBatch"
> attr(,"package")
> [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?
> 
> Best,
> 
> Georg
> 
> 
> sessionInfo()
> 
> R version 2.4.0 (2006-10-03) 
> x86_64-redhat-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> 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"
> 
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-- 
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber