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 [[alternative HTML version deleted]]

Ying, It appears you're using an old version of frma. If you update to the latest release or devel version, frma will return an ExpressionSet. Best, Matt On Mon, Oct 3, 2011 at 2:55 PM, Wang,Ying <ywang31 at="" mdanderson.org=""> wrote: > 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 at 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 > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880