Figure 7

Hybridization and RNA-quality characteristics of the GADPH and beta-actin control probe sets in the tissue (left) and rat-QC (right) data sets. Each data point refers to one array of the respective series. The abscissa provides the degradation level in units of the logged 3′/5′- mean intensity ratio of the respective control data sets. The vertical axes plot either sigma coordinates of the 3′- (green dots) and 5′- (blue dots) probe sets of the controls, or their mean (dark blue circles). The red and black dots mark the respective sigma-levels of non-specific binding and of saturation, respectively. The vertical orange lines indicate the constant quality threshold separating good (to the left) and poor (to the right) apparent RNA quality. The ‘threshold’ hooks (orange) refer to the same quality threshold. They however explicitly consider its decrease in the N- and sat-ranges of hybridization. Application of the constant threshold thus produces false positives together with true positives and true negatives (see also Figure12)