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To detect differential methylation between CpG loci in different HSCP populations, 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.
Figure 1. ANOVA setup dialog. Experimental factors listed on the left can be added to the ANOVA model. To set up an interaction, select two factors in the Experimental Factor(s) list. ANOVA models can be saved and resued using Save Model... and Load Model... buttons. Contrasts... allow for setting up group comparisons. Cross Tabs launches a web browser window with breakdown of samples across the factors. Advanced... enables fine tuning of the algorithm and the output
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