Additional file 2.

Differential methylation p value distribution of positive and negative CpGs between prostate cancer and normal samples for Dataset 3 before and after normalization/batch correction. The positive CpGs (85) were selected from genes frequently reported in the literature whose CpGs are hypermethylated in prostate cancer. The negative CpGs (358) were selected for housekeeping genes. A: After normalization and normalization/EB correction, the numbers of differentially methylated positive CpGs all increase compared to un-normalized data. B: The p values for negative CpGs are almost uniformly distributed and there is no indication of bias introduced from normalization and batch correction (the significant CpGs at p < 0.05 are all less than expected 18).

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