I successfully created the CDF package and made sure both the package and the datasets for the microarray were in the same part of the computer. I still got the following: AffyBatch object size of arrays=716x716 features (26 kb) cdf=AFLAVUSa520391F (??? affyids) number of samples=18 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain AFLAVUSa520391F Library - package aflavusa520391fcdf not installed Bioconductor - aflavusa520391fcdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch)