Control probes acts as surrogates for batch effects. (a) Heat map of a summary (see Materials and methods) of the control probes, with samples on the y-axis and control summaries on the x-axis. Samples were processed on a number of different plates indicated by the color label. Only columns have been clustered. (b) The first two principal components of the matrix depicted in (a). Samples partially cluster according to batch, with some batches showing tight clusters and other being more diffuse. (c) The distribution of methylated intensities averaged by plate. These three panels suggest that the control probe summaries partially measure batch effects. PC, principal component.