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Figure 5 | Genome Biology

Figure 5

From: A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

Figure 5

Workflow of CPACOR (incorporating Control Probe Adjustment and reduction of global CORrelation) for Epigenome-wide Association Studies using the Illumina HumanMethylation450 BeadChip. Signal intensities are filtered for multiple Quality Control criteria followed by quantile normalisation and calculation of beta values. In addition intensities from Illumina control probes are used to derive principal components (control-probe PCs). Based on beta values, proportions of white blood cell subpopulations are estimated and PCs are derived (from intermediary residuals; see Methods for details). To detect differential methylation regression analysis is performed for each methylation marker predicting disease status as a function of the (quantile normalised) beta value adjusted for technical and biological factors and PCs.

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