Dear R users: Thanks to you all, I am finding very useful previous questions and answers from other users. But I was not able to find out what I am doing wrong when trying to load the covdesc file. I have a folder in my directory that contains all 18 CEL files and also the covdesc (extension .prn - is this the right one?). Since I was able to run the gcrma normalization so the working directory maybe well set, what I got is the next: > raw.data <- ReadAffy() > gcrma.eset <- call.exprs(raw.data, "gcrma") Loading required package: AnnotationDbi Adjusting for optical effect..................Done. Computing affinities.Done. Adjusting for non-specific binding..................Done. Normalizing Calculating Expression > raw.data <- read.affy() ##read data in working directory Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './covdesc': No such file or directory > raw.data<- read.affy("covdesc") Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './covdesc': No such file or directory thanks in advance for any help. Miriam [[alternative HTML version deleted]]