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Open Access Highly Accessed Research article

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

Pan Du13*, Xiao Zhang2, Chiang-Ching Huang2, Nadereh Jafari4, Warren A Kibbe13, Lifang Hou23 and Simon M Lin13*

Author affiliations

1 Northwestern University Biomedical Informatics Center (NUBIC), NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA

2 Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA

3 The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA

4 Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA

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Citation and License

BMC Bioinformatics 2010, 11:587  doi:10.1186/1471-2105-11-587

Published: 30 November 2010

Abstract

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 Positive Rate (TPR) for both highly methylated and unmethylated CpG sites. Imposing a minimum threshold of difference can improve the performance of the M-value method but not the Beta-value method. We also provide guidance for how to select the threshold of methylation differences.

Conclusions

The Beta-value has a more intuitive biological interpretation, but the M-value is more statistically valid for the differential analysis of methylation levels. Therefore, we recommend using the M-value method for conducting differential methylation analysis and including the Beta-value statistics when reporting the results to investigators.