I think Bioconductor packages have not been able to read the newer Affy file formats (for good reasons explained in a post by Rafael I.). But I just got an e-mail from Affy saying that they are making a library available under LGPL (see below). So, just in case anyone who should know does not already know... File Parsers SDK - OPEN SOURCE We are pleased to announce the release of C++ source code for the parsing of Affymetrix CEL, CHP, CDF, BAR and BPMAP files. This souce code is being provided under the GNU Lesser General Public License (LGPL). Click here to download the SDK here