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 anova-1way_autosomal (autosomal) as the source spreadsheet from the left-hand panel
• Select LCLs vs. B cells 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 20
• Set OR Fold change < to -20
• Set p-value with FDR to 0.005
• Set file name as LCLs vs. B cells
• Leave the rest of the option set to defaults (Figure 1)
  
  

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

The new spreadsheet LCLs vs. B cells (LCLs vs. B cells) will open in the Analysis tab (Figure 2).