Fig. 5

Cross-platform data integration using RnBeads. a Distribution of DNA methylation levels for the same samples profiled across different assay platforms. b Principal component analysis of the assay comparison dataset. Point shapes and colors depict assay platforms and cell types, respectively. c–e Density scatterplots comparing replicates of prostate epithelial cells profiled using the EPIC assay (panel c); prostate epithelial cells profiled using the EPIC assay and WGBS (panel d); and prostate epithelial cells as well as a prostate cancer cell line profiled with the EPIC assay (panel e). Point density is indicated by blue shading. The 0.1% of CpGs in the most sparsely populated areas of the plot are shown as individual points. All plots are based on CpGs that were covered by all three assay platforms. Pearson correlation coefficients are shown below each diagram. NAF, non-malignant tissue-associated fibroblasts; CAF, cancer-associated fibroblasts; PrEC, prostate epithelial cells; LNCaP, prostate cancer cell line