Although the 450K and MethylationEPIC arrays were initially designed to analyze DNA methylation, they are essentially a dense SNP array and can thus be used for copy number analysis (Feber et al. 2014). The probe intensity data is easily parsed from the idat files by using the Additional Probe Data Spreadsheet Selection dialog (Figure 1) when importing the raw data. Examining the raw intensity data can also be useful for QA/QC purposes. 

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• Select Probe Intensity and Antilog Probe Intensity Values (Figure 2)
• Select OK to close the Advanced Import Options dialog
• Select Import to import the data and perform the selected normalization method
• Select the (_probe) spreadsheet from the spreadsheet tree
• Delete any samples with _detectionp names
• Create sample attributes, assign samples to the groups, and filter as described in Annotate and Filter Samplesfilter samples
• Select Transform from the main toolbar 
• Select Normalize to baseline 

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