Illumina’s MethylationEPIC array interrogates the methylation status of over 850,000 cytosines in the human genome. Since Because the MethylationEPIC array is closely related to the Infinium HumanMethylation450 BeadChip, the steps presented in this document can be applied to either platform. The analysis laid out in the tutorial is based on detection of differentially methylated CpG sites and their subsequent filtering and annotation. 

This tutorial illustrates how to:

Note: the workflow described below is enabled in Partek Genomics Suite version 7.0 software. Please fill out the form at www.partek.com/PartekSupport to request this version or use the Help > Check for Updates command to check whether you have the latest released version. The screenshots shown within this tutorial may vary across platforms and across different versions of Partek Genomics Suite.

Due to annotation changes, the results presented here may slightly differ over the time.

The data set accompanying this document consists of sixteen human samples processed by Illumina MethylationEPIC  BeadChip arrays. The data set is taken from a study of DNA methylation in human B cells and  B cells infected with Epstein-Barr virus (EBV). 

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The data files can be downloaded from Gene Expression Omnibus using accession number number GSE93373 or by selecting this link - Differential Methylation Analysis data set. To follow this tutorial, download the 32 .idat files associated with GSE93373  (note that two .idat files are generated for each array) and unzip them on your local computer using 7-zip, WinRAR, or a similar program. The .idat files can be downloaded individually by selecting the links for each sample or all together in one zipped folder by selecting the GSE93373_RAW.tar file at the bottom of the page.