Hi Hui, > Since the cdf I was using doesnot belong to any of the standard ones, could > that be the problem? If yes, how do I attach my own cdf? The easiest way is to convert the CDF file into what amounts to a large hash table. Use the package "makecdfenv", and in there, the function make.cdf.package, for this (from the Bioconductor website, and for nicer features, under the section "Developmental Packages"). Then install the package "testcdf", and try to run read.affybatch again. Best regards Wolfgang ---------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany ----------------------------------------