Raw microarray data collected using the Affymetrix platform were normalized using the Robust Multichip Array (RMA) method [28]. Raw microarray data collected using Illumina platform were normalized using the Rank Invariant method and background subtraction protocols provided by Illumina as part of the BeadStation software suite. Both sets of expression data were then re-normalized using a modified Z score described in a previous publication [29]. We calculated the log base 2 of the normalized values, computed Z scores for each array, multiplied the Z scores by 2, and added an offset of 8 units to each value. This transformation yields a set of Z-like scores for each array that have a mean of 8, a variance of 4, and standard deviation of 2. The advantage of this modified Z score is that a two-fold difference in expression corresponds approximately to a 1 unit change.
