I want to pre-process some microarray datasets and I would like to know how I can compare them if the datasets are from different platforms. Specifically, one of the datasets is the Hedenfalk et al. 2001 dataset in which the gene expression values are given as the ratio of Cy5/Cy3 intensities. The other datasets I have are of Affymetrix-type and I have been using RMA preprocessing (Bioconductor) for them. As far as I understand the RMA preprocessing outputs the expression values as log2 transformed values. Since I am new on the topic, could you explain me how I can compare (or what steps are further needed) the RMA processed data with the Hedenfalk data?
Thanks a lot,