Why does methylation data have bimodal distribution?

Question

[gaol]

I'm analyzing the HM450K array methylation data and I'm wondering why does some probes have this bimodal distribution? I've already removed probes that have SNPs or have SNPs within 10 bp. Also are there any suggestions for modeling methylation with this distribution as the outcome? Thank you!

[karl.stamm]

LABEL YOUR AXES. WE CANT TELL WHAT YOURE TALKING ABOUT IF THE X AXIS IS BLANK

[gaol]

This is a histogram of methylation at one CpG probe. It's showing the beta values. The X axis is the methylation data ranging from 0 to 1

[karl.stamm]

Okay, great. So what is a methylation beta value? Beta is a generic parameter that means something different in each situation, but in your case it might be a probe intensity ratio, and the bi-modal indicates "off" and "on" signals.