To analyze differences in methylation between our experimental groups, we need to create a list of deferentially methylated loci. 

• Select Create Marker List from the Analysis section of the Illumina BeadArray Methylation workflow
• Select 1/anova-1way_autosomal_only (ANOVA-1way_autosomal_only) as the source spreadsheet from the left-hand panel
• Select Naive shPOU5F1 and Naive shNANOG and Primed shCTRL vs. Naive shCTRL from the Contrast: find genes that change between two categories section of the ANOVA Streamlined tab of the List Manager dialog
• Set Fold change > to 3
• Set OR Fold change < to -3
• Leave the rest of the option set to defaults (Figure 1)
  
  

• Select Create
• Select Close to exit the List Manager dialog

You may want to save the project before proceeding to the next section of the tutorial.