An important characteristic of this dataset is the normalization procedure. For each spot and in each channel (Cy3 and Cy5), True et al. substracted the median background intensity from the median foreground intensity, and subsequently the log ratios of cancer expression to benign expression were computed. These ratios were obtained by first dividing the background-subtracted intensities (Prostate Cancer/Benign) and then taking the logarithm base 2. In the case that the median background intensity was greater than the median foreground intensity, the spot was considered missing. We refer to the original publication for the other aspects of imputation, spot quality and filtering, but, like in Lapointe et al's study, they also filter to keep informative (expression ratios of benign versus cancer should at least be 1.5-fold or greater in at least half of one of the Gleason groups as one of the selection criteria).