Hi everybody, I have recently installed oneChannelGUI and all the Affymetrix Power Tools (apt-1.6.0) in a PC. The installation went OK. I am trying to analyze Affymetrix Rat exon chips, I wanted to import CEL files and apply iter-plier for gene level and rma-sketch for exon level intensity summaries. After defining all the paths (ATP, library, working directory and targets file) and the summarization method, I've got the following error reports in the R console and the CEL files were not imported. Gene level probe sets summary started Gene level probe sets summary ended Error in as.matrix(my.exons) : no function to return from, jumping to top level In addition: Warning messages: 1: In system(gene.iterplier, wait = T) : C:/Program not found 2: In dir(tempOut) : list.files: 'D:/Researchers/Weizmann Institute/Biological chemistry/.../out72ae2cd6' is not a readable directory 3: In file(file, "r") : cannot open file 'D:/Researchers/Weizmann Institute/Biological chemistry/.../out72ae2cd6/', reason 'No such file or directory' Do anybody has any idea what went wrong and how to repair it? Thanks, Esti -- Ester Feldmesser, Ph.D. Bioinformatics Unit, Department of Biological Services Weizmann Institute of Science Levine Building, Room 110 phone: +972-8-934-2614 email: ester.feldmesser at weizmann.ac.il