The data set accompanying this document consists of eight human samples processed by Illumina MethylationEPIC  BeadChip arrays. The data set is taken from a study of DNA methylation in human pluripotent stem cells (hPCS) (Lee et al. Cell Rep 2017) and can be downloaded from Gene Expression Omnibus using the following accession number: GSE95531. To follow this tutorial, download the 16 .idat files associated with GSE95531 (note that two .idat files are generated for each array) and unzip them on your local computer. A discussion on import of files processed by Illumina’s Genome Studio package can be found in Appendix A.

To load the .idat files to Partek Genomics Suite go to the Workflows drop down list, choose Methylation and then select Illumina BeadArray Methylation sub-workflow. That will open Illumina BeadArray Methylation workflow (Figure 1). Select Import Illumina Methylation Data and specify to Import human methylation 450/850 .idat files and push OK.

In the next dialog, use Browse… to point to the folder in which the .idat files were unzipped and use the Add File > button to move the .idat files to the box on the right (i.e. idat Files to Process; Figure 2). Select Next > to proceed.

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