Methylation Array in R

An introduction to methylation array analysis: Workflow for analysing Infinium MethylationEPIC data

Lead trainer: Stella Liu, Melbourne Bioinformatics, The Univeristy of Melbourne Workshop Description: DNA methylation is an epigenetic modification involved in gene regulation, development and disease. Comparing methylation patterns between biological conditions can help us understand how these processes change. This workshop introduces Illumina EPIC methylation arrays and shows how to analyse their data using R and Bioconductor packages. Starting with raw IDAT files, we will work through sample quality control, probe filtering, normalisation, and exploratory visualisation before identifying differentially methylated probes and regions. Learning objectives: The aim is to show you how to go from raw methylation array files to identifying differences in methylation between groups. We will explain each step so that you will understand how to perform the analysis. By the end of the workshop, you will be able to: Import methylation array data and organise sample information. Apply normalisation and understand its assumptions. Assess sample quality and filter unreliable probes. Use visualisation to explore sample relationships and potential technical variation. Identify and interpret differentially methylated probes and regions. Recognise limitations of the experimental design and analysis when drawing biological conclusions. Target Audience: Anyone who: Is familiar with DNA methylation and understands its basic principles. Is interested in learning how to analyse methylation array data. Knows the basics of R. Has a basic understanding of statistics, including hypothesis testing. Eligibility: This free workshop is available to staff and students at The University of Melbourne and its affiliated institutes.

You must register for this event using an affiliated institutional email address or your registration may be cancelled. Prerequisites and Requirements: This workshop requires particpants to have R experience as a prerequisite. This is an in person hands-on workshop and attendees must bring their own computers (laptop chargers also recommended). The following is required:

Access to internet via UniWireless or Eduroam

Web browser (Firefox or Chrome recommended) Install RStudio: https://posit.co/downloads Install R: https://www.r-project.org/ Access: If you require any further information, or have any access requirements in order to participate in this workshop, please contact us as soon as possible to discuss your requirements:

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Important Policy Update: Starting 1 August 2025, participants who miss two or more workshops without proper notice (less than 48 hours or attending under 50%) within 12 months will…