Additional file 1.

Fitted lowess curves of M-A plot for Dataset 2 and 3. X-axis is for the methylation mean across all samples and Y-axis is the difference between each sample and the mean. Each curve represents a sample; red and green mark samples from two different batches. A: Dataset 2, red for Chip11 and green for Chip12. B: Dataset 3, red for Chip54 and green for Chip36. Bothe datasets show clear non-linear "intensity dependent" biases.

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Sun et al. BMC Medical Genomics 2011 4:84   doi:10.1186/1755-8794-4-84