Figure 1

Distribution of signal intensities. (A) Training samples and fresh-frozen xenografts processed according to the Affymetrix One-Cycle protocol (B) training samples and fresh-frozen xenografts processed according to the MessageAmp Premier protocol (C) FFPE xenografts processed according to the MessageAmp Premier protocol. For each sample, the 5^th, 25^th, 50^th, 75^th, and 95^th percentile of the MAS5.0 normalized signal values for all probes on the microarray was calculated. The resulting number was divided by the scaling factor. The logarithm to the base 2 of the resulting quotient was determined. These numbers are visualized by the box-and-whisker plots.