We are planning to release a package to take some Illumina-specific features for the data transformation (not log2) and normalization (not quantile) process. We are looking for beta testers before sending the package to Bioconductor. If you are interested, please send me an email to s-lin2 at northwestern.edu We have finished the alpha test with a golden standard data set. We are working on the tutorial now. The beta release will be within a week. Thanks! Simon