As a complement, another mode of data analysis was developed at SSI, where data was processed using the NimbleScan software program (NimbleGen, Roche). A mean of intensities for each probe-set was calculated. Outlier intensities within each probe-set were filtered out when signals were more than 3 standard deviations from the mean of the probe-set. A signal threshold was defined as the 99 th percentile of the random control intensities, and every probe-set mean containing more than 10 signals above this threshold was considered as a positive signal.