Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

Background: High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes. The microarray-based Infinium methylation assay by Illumina is one platform for low-cost high-throughput methylation profiling. Both Beta-value and M-value statistics have been used as metrics to measure methylation levels. However, there are no detailed studies of their relations and their strengths and limitations. Results: We demonstrate that the relationship between the Beta-value and M-value methods is a Logit transformation, and show that the Beta-value method has severe heteroscedasticity for highly methylated or unmethylated CpG sites. In order to evaluate the performance of the Beta-value and M-value methods for identifying differentially methylated CpG sites, we designed a methylation titration experiment. The evaluation results show that the M-value method provides much better performance in terms of Detection Rate (DR) and True Positiv...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A. Kibbe, Lifang Hou, Simon M. Lin
• Keywords: BMCBI 2010, Business, CpG Sites, M-value Method, Methylation