Dear all,

It's the first time that I use the frma package. I'm working on data from Affymetrix GeneChip Mouse Genome 430 2.0 arrays.  I expected an ExpressionSet to be produced by using the "frma" function. But I got PLMset data instead. I couldn't use exprs() function on what I got and I couldn't use pset2eset to convert my PLMset data to ExpressionSet. Any help will be highly appreciated. Here is my code and the result I got. Attached please find the package versions I'm using. Thank you all.

Best,

Ying

>library(affy)
>library(simpleaffy)
>library(frma)
>library(mouse4302frmavecs)

First I read in the raw data.
> ab <- ReadAffy(filenames=fnames, ...)

Then run fRMA on the raw data
> x.frma=frma(ab)
> x.frma
Probe level linear model (PLMset) object
size of arrays=1002x1002
cdf=Mouse430_2 (45101 probeset ids)
number of samples=8
number of probesets=45101
number of chip level parameters for each probeset=8
annotation=mouse4302
PLMset settings
Creating function:
Preprocessing
Background Correction=Error in if (object@model.description$preprocessing$background) { :
  argument is of length zero


Now the problem occurs

> dim(exprs(x.frma))
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "exprs", for signature "PLMset"

> x.frma.eset=PLMset2exprSet(x.frma)
Error in validObject(.Object) :
  invalid class "ExpressionSet" object: 1: row numbers differ for assayData members
invalid class "ExpressionSet" object: 2: sample numbers differ for assayData members



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