Fig 2. Comparison of BEclear, SVA and Functional normalization (minfi package) with respect to the number of BE-genes still remaining after the correction of adjacent normal BRCA data.

Batch affected genes are defined as genes with (1) median difference above 5% of β-value distribution and (2) showing a statistically significant difference in this batch compared to all other batches with (p-value ≤ 0.01) according to the Kolmogorov-Smirnov test.