Hi Richard, You need to change a little bit the code. round(ReadAffy(filenames = paste(celFolder, i, sep = "/"))@exprs) to round(exprs(ReadAffy(filenames = paste(celFolder,i, sep = "/"))))) in celExtNorm and celExtract functions. Thanks for Ben told me this before. Pingzhao ------------------------------------- I'm getting a mysterious error message "no slot of name "exprs" for this object of class "AffyBatch"" Anybody got any ideas on what crime I committed? I got the latest greatest Bioconductor stuff yesterday. The gory details ... -bash-3.00$ uname -a Linux xxxxx.yyy.nih.gov 2.6.9-42.0.3.ELsmp #1 SMP Mon Sep 25 17:24:31 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux -bash-3.00$ R WARNING: ignoring environment value of R_HOME R version 2.5.1 (2007-06-27) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 ... [blah blah blah ] .... [Previously saved workspace restored] > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio > library(PLASQ500K) Loading required package: GLAD Loading required package: aws [1] "Have fun with GLAD" > pscn(NspFolder=NULL, StyFolder="/work/joe/TUMOR", normNspFolder=NULL, normStyFolder="/work/joe/NORMAL") [1] "Reading in Normal .cel files" [1] "Reading Files" [1] "XMapping250K_Sty_A02_47432.CEL" [1] "now readaffy" Error in round(ReadAffy(filenames = paste(celFolder, i, sep = "/"))@exprs) : no slot of name "exprs" for this object of class "AffyBatch" >