Methylation, the addition of a methyl group to a CG dinucleotide of the DNA, is the most extensively studied epigenetic mark. Although it can be measured in many ways, the most popular platform for measuring methylation has been the Illumina HumanMethylation450 (450k) array. In this workshop, we will introduce the features of the 450k array and how to analyse the methylation array data using R. We will cover the steps involved in the standard 450k analysis pipeline including: quality control, filtering, normalization, data exploration and probe-wise differential methylation array analysis. We will also cover other approaches such as differential methylation analysis of regions, differential variability analysis and gene ontology analysis. Finally, we will provide some examples of how to visualise methylation array data.