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• Select Create Marker List from the Analysis section of the Illumina BeadArray Methylation workflow
• Select the Advanced tab Select LCLs vs. B cells (Figure 1)
  
  

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• Name this list; we have chosen differentially regulated
• Select OK

The criteria differentially regulated has been added to the Criteria list (Figure 3). 

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• Name this list; we have chosen <0.005
• Select OK

Both differentially regulated and <0.005 are listed in the Criteria panel. We can use the Combine criteria tools to generate a single combined filter. 

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• Select OK from the List Creator dialog to generate a list using the LCLs vs. B cells filter
• Select Close to exit the List Manager dialog

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• 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 to exit the list manager

The new spreadsheet LCLs vs. B cells (LCLs vs. B cells) will open in the Analysis tab. You may want to save the project before proceeding to the next section of the tutorial.

• Select File from the main taskbar
• Select Save Project... 
• Give the project a name; we chose Methylation Tutorial 
• Select Save

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