arrays, probably as a consequence of longer probes on the former platform. Older arrays tend to perform less well than newer arrays from the same producer, with the exception of CNV focused arrays (Illumina 660W and Agilent 2X244K) where the large fraction of probes located in regions deviating from a copy number of two affects the global variance statistic. For all platforms, some hybridizations were discarded under quality control procedures (Supplementary Methods). For the Affymetrix 500K platform, experiments performed for the 250K Sty assay failed quality control, and we therefore used only results from the 250K Nsp assay for further analyses.
