Array hybridizations (Agilent-014850 4×44 k arrays, GPL4133) were performed at The University of Chicago, Argonne National Labs high throughput genome analysis core facility, according the manufacturers instructions. The Agilent FE software was used to extract feature intensities and to flag saturated, non-uniform, and outlier features. Probe intensity was adjusted by subtracting background intensity using the minimum method [54], [55] and quantile normalized between arrays [56]. Dixon's outlier test was used to remove 13 arrays (out of a total of 517) based on total number of flagged probes, intra-array variance, inter-array variance, biological replicate variance, and spike-in linearity [57].
