Figure 2

Dataset 2 before and after normalization and batch correction. A: The density plot of average β values for two chips of samples. All samples on Chip12 shift to the left, more CpGs with lower methylation values. B: PCA plot (first two components) for the 24 samples using 26,486 CpGs after excluding CpGs in sex chromosomes; samples on each chip cluster closely with the first component explaining 50.3% of variance. C: Density plot of lumi normalized data. The distribution bias has been greatly reduced but a significant portion remains. D: PCA plot of lumi normalized data still shows clear sample separation by batches using 26,486 CpGs after excluding CpGs in sex chromosomes. E: Density plot of average β after ABnorm. The distribution bias has been successfully removed. F: PCA plot of ABnorm data shows the clear remaining batch effects using 26,486 CpGs. G: The profiles of selected 20 CpGs that are associated with the batch effects after normalization. X-axis-samples ordered by Chip (11 or 12). Y-axis-methylation average β. Each line represents one CpG across samples. These CpGs are either all higher or lower on one chip than another. H: The profiles of the same 20 CpGs as G after normalization and EB correction. The systematic differences between the two chips have been removed.