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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. 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