The result of this is a single value for each probe per array. To normalize expression values across arrays, we performed quantile normalization as previously described58. Briefly, we ranked each array from lowest to highest expression. For each rank, we computed the average expression and each experiment with this value at the associated rank. For each probe, we computed the difference between the second smallest expression value and the second largest expression value. If this difference was less than 2, we filtered the probe. This metric was chosen to eliminate bias due to single sample outliers.
