Can I compare Beta values calculated in BeadStudio to percent methylation calculated using other technologies?
The Beta value is unique to the Illumina platform and can range from 0 to 1, with 0 indicating no methylation and 1 indicating complete methylation at a given locus. Importantly, the Beta value reports on the intensity ratio between methylated- and nonmethylated-specific assays for each CpG site. Since assay performance can vary between loci, this ratio does not consistently report percent methylation.
