Illumina’s MethylationEPIC array interrogates the methylation status of over 850,000 cytosines in the human genome. Since the MethylationEPIC array is closely related to the Infinium HumanMethylation450 BeadChip, the steps presented in this document can be applied to either platform.

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 The analysis laid out in the tutorial is based on detection of differentially methylated CpG sites and their subsequent filtering and annotation.

• Importing and normalizing methylation data
• Annotating the samples
• Performing exploratory data analysis
• Detecting differentially methylated loci
• Visualizing the methylation at each locus
• Obtaining methylation signatures
• Biological interpretation
• Detecting differentially methylated CpG islands regions