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- Select Create Marker List from the Analysis section of the Illumina BeadArray Methylation workflow
- Select the Advanced tab Select LCLs vs. B cells (Figure 1)
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- Name this list; we have chosen differentially regulated
- Select OK
The criteria differentially regulated has been added to the Criteria list (Figure 3).
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- 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.
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- 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
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- 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
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