Probe set-specific variance is preserved across experimental paradigms. In the left panel, the probe set-specific standard deviation (SD) derived from two of the experimental paradigms (cells exposed to troglitazone or GW7845, see Methods) was plotted, and probe sets that had high (top 5 %, red) or low (bottom 5 %, blue) variability were identified. In the right panel, the SD of each probe set that was identified in the left panel was determined using the third experimental paradigm (control). Probe sets with average variability lie along the line α
= 1 (green). The main figure depicts the entire data set, and the inset shows the area up to signal intensity of 5000, magnified for clarity. Using chi-square analysis we confirmed that the SD for the low and high variability probe sets, determined by the left panel, was highly predictive of the respective SD in the right panel (p < 0.0001).