Mean/SD plots of the RMA values for all probeset data pairs for the 137 hybridizations of the rat dataset (a) without normalization, (b) with quantile normalization and (c) with 75% percentile normalization. The signal level scale is shifted by 28 for the 75% percentile normalization data (c). Separate symbols denote probeset data pairs (mean, SD) for the spiked-in hybridization (▲) and polyA+ (▲) controls and for the cRNA degradation (●) and endogenous/housekeeping (○) internal controls. Non-control (background) probesets and the moving mean derived from them are denoted with gray-filled symbols, (•) and (•), respectively. Select spiked-in polyA+ control and RNA degradation probesets are labeled according to the abbreviations in Additional File 1: Supplemental Table S2.