Each row of the spreadsheet (Figure 1) corresponds to a single sample. The first column is the names of the .idat files and the remaining columns are the array probes. The table values are β-values, which correspond to the percentage methylation at each site. A β-value is calculated as the ratio of methylated probe intensity over the overall intensity at each site (the overall intensity is the sum of methylated and unmethylated probe intensities). 

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The Create categorical attribute dialog (Figure 3) allows us to create groups for a categorical attribute. By default, two groups are created, but additional groups can be added. 

• Select New Group twice to add two additional groups
• Set Attribute name: to hPSC 
• Rename the four groups Primed, Naive, shPOU5F1, and shNANOG
• Drag and drop the samples from the Unassigned list to their groups as listed in the table below

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There should now be four groups with two samples in each group (Figure 4).

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A new column as been added to spreadsheet 1 (Differential Methylation Analysis) with the experimental group of each sample (Figure 5). 

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