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To come up with a list of differentially methylated loci, proceed to the workflow and select Create Marker List. That will open the List Manager functionality and you will be on the ANOVA Streamlined tab. Factors in the model are listed in the top section, contrasts specified in the model are in the middle, while the filter settings are at the bottom.

Select shNANOG vs Primed contrast to see the current filter configuration. By default, both fold-change and p-value with false discovery rate correction are applied, with the number of CpG loci passing the filter given as # Pass. 

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