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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 the Advanced tab (Figure 1)

Genomics Suite Documentation > Create a marker list > 2017-07-24 11_37_47-List Manager.png

Select Specify New Criteria to launch the Configure Criteria dialog
Select female_only/anova-1way_autosomal (autosomal) from the Spreadsheet drop-down menu
Select 12. Estimate(LCLs vs. B cells) from the Column drop-down menu
Set Include values to less than or equal to with -5 and greater than or equal to with 5 (Figure 2)

Genomics Suite Documentation > Create a marker list > 2017-07-24 09_30_06-Configure Criteria.png

Name this list; we have chosen differentially regulated
Select OK

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

Genomics Suite Documentation > Create a marker list > 2017-07-24 09_30_18-List Manager.png

Select Specify New Criteria
Select female_only/anova-1way_autosomal (autosomal) from the Spreadsheet drop-down menu
Select 6. p-value(LCLs vs. B cells) from the Column drop-down menu
Set Include p-values to significant with FDR of at 0.005 (Figure 4)

Genomics Suite Documentation > Create a marker list > 2017-07-24 10_23_51-Configure Criteria.png

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.

Select Intersection (And) from Combine criteria to create a combined filter
Name the new filter; we have chosen LCLs vs. B cells
Select Save List (Figure 5)

Genomics Suite Documentation > Create a marker list > 2017-07-24 10_24_02-List Manager.png

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

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.