The BioPNG Gel Plot. (A) The gel plot of the original scanned data for the Renal Cell Carcinoma Affymetrix X3P GeneChip. The arrow indicates a chip with a corrupted file format, causing the intensity values to be read incorrectly. The Bioconductor program that parsed the chips did not catch this error, but it became clear after visualizing the intensity distributions. (B) The gel plot of the normalized and artifact-replaced data output by caCORRECT. These distributions are clearly well-aligned, but the same data parsing problem persisted without causing any post-processing algorithms to generate errors.