Dear list, I calculated correction values for each probe cell. I do the following: Reading the cel-files in an AffyBatch: Expfiles <- c("1.CEL","2.CEL","3.CEL","4.CEL") chips = ReadAffy(filenames = Expfiles) Performing background correction: Chips.bg.mas <- bg.correct(chips, method ="mas") Performing normalization: Chips.norm.quantile.mas <- normalize(Chips.bg.mas, method ="constant") Performing correction Chips.norm.quantile.mas at exprs <- Chips.norm.quantile.mas at exprs*correctionMAS ### Not done when I tried express.summary.stat.. performing pmcorrection Chips.PM.Mas <- pmcorrect.mas(Chips.norm.quantile.mas) And now I want to use the method "computeExprSet" to calculate an ExprSet. But I receive the following error: error in ...... no direct or inherited method for function '...' for this call The same when I try error in express.summary.stat(Chips.norm.quantile.mas, summary = "mas", : no direct or inherited method for function 'express.summary.stat' for this call Any ideas ? Gunther H?ning

Hi Gunther, The problem with doing your own method is that you have to watch closely what you are doing, and be very familiar with the help pages. The H?ning wrote: > Dear list, > > I calculated correction values for each probe cell. I do the following: > > Reading the cel-files in an AffyBatch: > Expfiles <- c("1.CEL","2.CEL","3.CEL","4.CEL") > chips = ReadAffy(filenames = Expfiles) > > Performing background correction: > Chips.bg.mas <- bg.correct(chips, method ="mas") > > Performing normalization: > Chips.norm.quantile.mas <- normalize(Chips.bg.mas, method ="constant") > > Performing correction > Chips.norm.quantile.mas at exprs <- Chips.norm.quantile.mas at exprs*correctionMAS Not sure what correctionMAS is here, but let's assume it is either a scalar or a vector. > > ### Not done when I tried express.summary.stat.. > performing pmcorrection > Chips.PM.Mas <- pmcorrect.mas(Chips.norm.quantile.mas) Now if you do class(Chips.PM.Mas), you will get 'matrix'. > > > And now I want to use the method "computeExprSet" to calculate an ExprSet. Unfortunately, the arguments for computeExprSet are x: a 'AffyBatch' holding the probe level informations to generate the expression values. But you are passing a matrix, hence you get the following error. > > But I receive the following error: > error in ...... > no direct or inherited method for function '...' for this call > > The same when I try > > error in express.summary.stat(Chips.norm.quantile.mas, summary = "mas", : > no direct or inherited method for function 'express.summary.stat' for this call Again, the help page for this function states: Arguments: x: a ('ProbeSet' But you are passing an AffyBatch, not a ProbeSet. NB - this is an old function (as are all functions that take a ProbeSet as their input), and may not work as intended any longer. Most of the 'roll-your-own' functions in the affy package were developed in the days when people were still arguing over the best method to use for affy data. In the intervening time it appears (to me at least) that people have settled on their favorite method, so these legacy functions are no longer used as much and hence might not be maintained as rigorously as e.g., rma(). In fact, last I heard Rafa was considering taking expresso() and friends out of the affy package because they don't appear to be used much, and are a pain to maintain. Best, Jim > > > Any ideas ? > > Gunther H?ning > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.