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 LCLs vs. B cells (Figure 1)
  
  

Figure 1. Creating a list of significantly differentially methylated loci

• 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.

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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