Dear List,

I am working on a data set generated using Illumina's methylation 450K array. The goal is to identify regions that are differentially methylated between cases and controls. It seems that people are using beta value difference and Wilcoxon Rank Sum test for this kind of analysis. My question is what will be a good cutoff to use for the beta value difference. I have seen people using 0.2, but not sure whether that is just generally accepted or there is other approaches that are more statistically sounding. How to justify if a lower beta value difference, e.g. 0.1,  is to be used?

Any suggestions will be highly appreciated.

Nancy Chen
Biomedical Informatics Specialist
City of Hope



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