Figure 8

Examples of artifacts present for biomarker identification analysis. Images are heat maps of residuals for two pairs of arrays, with red color indicating higher-than-expected probe intensity, and blue color indicating lower-than-expected probe intensity. Heat maps such as these reveal the intensity and type of artifacts after caCORRECT normalization and artifact identification, but before removal. Panels A and B show naturally occurring artifacts on two chips from the Schuetz et al. dataset. Blue color in the upper right quadrant of panel A indicates data in this region is artificially low. Multiple small compact artifacts, both red and blue, can also be seen. Panel B shows more examples of naturally occurring artifacts, including a large artifact on the right edge of the chip. In panels C and D respectively, synthetic circle-shaped hot-spot and black-hole type artifacts have been applied to the same chips from panels A and B. The artifact in C appears red due to its artificially high probe intensity values. In panel D, the synthetic black-hole artifact is visible as a blue circle.