Analysis of complex methylation data

The development of multiple DNA methylation analysis techniques, including higher-throughput assays, has resulted in data structures of increasing complexity and diversity. Here, we discuss the general principles of DNA methylation analysis and propose a nomenclature for the various types of methylation analysis. We briefly outline several DNA methylation analysis techniques and discuss how these different technologies affect the structure of the resulting methylation data. We then describe the basic statistics and bioinformatic principles relevant to the analysis of simple and complex methylation data. (C) 2002 Elsevier Science (USA). All rights reserved.