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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)

Genomics Suite Documentation > Create a marker list > image2017-12-26 11:30:29.png

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.