As of: affy 1.4.2 (in the developer section) - Binary cel files should now be read properly by ReadAffy()/read.affybatch(). - You may mix and match text, gzipped text (if supported on your platform) and binary cel files in a single call to ReadAffy()/read.affybatch(). Attempts will be made to automatically determine the format of each file and process appropriately - The compress flag is now ignored by ReadAffy()/read.affybatch() Thanks, Ben