The characterization of aberrant DNA methylation is emerging as a key part of the study of cancer development and phenotype. The technical advancements and decreasing costs of methods for high-throughput profiling of DNA methylation have brought about a high interest in the use of such methods in disease association studies. Here we discuss the principles for DNA methylation analysis using data from the Infinium DNA methylation BeadChip assays and describe the computational steps and statistical considerations going from processing of the raw array data to analysis of differential methylation. Moreover, we provide detailed guidelines on how to perform tumor subtype classification based on DNA methylation signatures.
