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• Select Defect Differential Methylation from the Analysis section of the Illumina BeadArray Methylation  workflow
• Select 2. Cell Type Type from the Experimental Factor(s) panel 
• Select Add Factor > to move 2. Cell Type to the ANOVA Factor(s) panel (Figure 1)
  
  

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By default, the fold-change value for each contrast will be calculated with the upper group as the numerator and the lower group as the denominator. Selecting Estimate will also include the difference in methylation levels between the groups at each CpG site in the output. These values will be needed later in the tutorial. 

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