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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 anova-1way_autosomal (autosomal) as the source spreadsheet from the left-hand panel
Select LCLs vs. B cells 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 20
Set OR Fold change < to -20
Set p-value with FDR to 0.005
Set file name as LCLs vs. B cells
Leave the rest of the option set to defaults (Figure 1)

May I suggest filtering by Estimate, instead? Fold-change is not typical for methylation studies.

Genomics Suite Documentation > Create a marker list > 2017-07-05 12_10_59-List Manager.png

The new spreadsheet LCLs vs. B cells (LCLs vs. B cells) will open in the Analysis tab (Figure 2).

You may want to save the project before proceeding to the next section of the tutorial.