[BioC] ExpressionSet, fitPLM confusion

[Georg Otto]

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"