Figure 3

Dataset 3 before and after normalization and batch effect correction. A: Box plot of raw average β for two chips of 24 samples. The medians between the two chips are similar, but the 3rd quartile values of Chip36 are much lower than Chip54. B: Box plot for the two chips of 24 samples after lumi normalization. C: The density plot of average β for 24 samples before normalization colored by batches. The distribution differs obviously between the chips. D: The density plot of "lumi" normalized average β for 24 samples shows a large portion of batch effects not corrected. E: unsupervised clustering using all 27,578 CpGs before normalization and EB correction shows the clear separation of samples by chips (Chip54 or Chip36); samples from the same tissue type tend to cluster within the same batch (* for normal prostates and others for tumors). F: unsupervised clustering after normalization and EB correction using all 27,578 CpGs shows the separation between batches is removed; samples from the same tissue type cluster closely (* for normal prostates and others for tumors). G: Methylation profiles of selected 20 CpGs that are significantly associated with the batch effects after normalization, showing the dramatic differences between the two chips. The letter "T" and "N" on x-axis represent tumor and normal sample. H: The methylation profiles of the same 20 CpGs as G after the additional EB correction. The systematic biases are successfully removed.