Figure 4.

Differences in β value distributions produced by Infinium I and II probes. (a) Density distributions of β values produced by Infinium I (solid line) and II (dashed line) probes for unmethylated (blue), hemi-methylated (purple) and methylated (red) reference standards (Std.). The difference in β value distribution between the Infinium I and II probes seen in the raw data can be adjusted for using the SWAN method. (b) The median and inter-quartile range of β value distributions for Infinium I and II probes is more similar when SWAN is applied to 450k data. (c) The differences in β value distributions produced by the different probe types can result in aberrant overall β value distributions, as seen in this normal human DNA sample. Applying the SWAN method results in an improvement in the overall β value distribution.