Create a marker list

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)

Figure 1. Advanced options for list creation

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)

Figure 2. Creating a filter to include loci with greater than 5x change in methylation status between LCLs and B cells

Name this list; we have chosen differentially regulated
Select OK

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

Figure 3. The differentially regulated criteria has been added

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)

Figure 4. Creating a filter that sets the significant with FDR cutoff at p<0.005

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)

Figure 5. Combining two criteria to make a more sophisticated filter

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.

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