• Store the 16 32 .idat files at C:\Partek Training Data\Differential Methylation Analysis or to a directory of your choosing. We recommend creating a dedicated folder for the tutorial.

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• Select Add File(s) > to move the files to the idat Files to Process pane of the Import Illumina iDAT Data dialog (Figure 6)
  
  

• Select Next >

The following dialog (Figure 7) deals with the manifest file, i.e. probe annotation file. If a manifest file is not present locally, it will be downloaded in the Microarray libraries directory automatically. The download will take place in the background, with no particular message on the screen and it may take a few minutes, depending on the internet connection. In the future, you may want to reanalyze a data set using the same version of the manifest file used during the initial analysis, rather than downloading an up-to-date version. To facilitate this, the Manual specify option in the Manifest File section allows you to specify a specific version. For this tutorial, we will use the latest available manifest file.

By default the output file destination is set to the file containing your .idat files and the name matches the file folder name. The name and location of the output file can be changed using the Output File panel. 

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The imported and normalized data will appear as a spreadsheet 1 (Differential Methylation Analysis) (Figure 9)

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