Figure 9

Within- and between-platform variance components for the oligo (red) and Agilent (green) platforms, as a function of average log fold change. The total variation between platform can be shown to be made up of the variation within each platform plus the variation between platforms which arises from different probe technologies and matching probes across technologies. It can be seen that the variance from between platform measurements is much larger than the variation within any given platform. As expected, the disagreement increases as the magnitude of the fold change increases.