To detect differential methylation between CpG loci in different HSCP populations, experimental groups, we can perform an ANOVA test.

• Select Defect Differential Methylation from the Analysis section of the Illumina BeadArray Methylation  workflow
• Select 2. Statefrom the Experimental Factor(s) panel of the ANOVA of Spreadsheet 1 dialog
• Select Add Factor > to move 2. State to the ANOVA Factor(s) panel 
• Repeat for 3. shRNA treatment
• Select 2. State and 3. shRNA treatment from the Experimental Factor(s) panel by holding the Ctrl key on your keyboard and selecting both 
• Select Add Interaction > to add the interaction between 2. State and 3. shRNA treatment 
• Select Contrasts... 
• 
  

go to Analysis > Detect Differential Methylation. In the ANOVA dialog (Figure 1), select Add Factor to move the factor 2. HPSC from Experimental Factor(s) to the ANOVA Factor(s) box.

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