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• 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
• Set file name as CpG of interest
• Leave the rest of the option set to defaults Select LCLs vs. B cells (Figure 1)
  
  

• Leave Include size of the change selected and set to Change > 2 OR Change < -2
• Leave Include significance of the change selected  and set to p-value with FDR < 0.05
• Select Create
• Select Close Close to exit the List Manager dialogthe list manager

The new spreadsheet Naive_shPOU5F1_and Naive_shNANOG_and_Primed_shCTRL_vs_Naive_shCTRL (CpG of interestLCLs vs. B cells (LCLs vs. B cells) will open in the Analysis tab (Figure 2).  

It is best practice to occasionally save the project you are working on. Let's take the opportunity to do this now. 

• Select File from the main command toolbar
• Select Save Project...
• Specify a name for the project, we chose Methylation Tutorial, using the Save File dialog
• Select Save to save the project

Saving the project saves the identity and child-parent relationships of all spreadsheets displayed in the spreadsheet tree. This allows us to open all relevant spreadsheets for our analysis by selecting the project file. 

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