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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
It is best practice to occasionally save the project before proceeding to the next section of the tutorial.you are working on. Let's take the opportunity to do this now.
- Select File from the main command toolbar
- Select Save Project...
- Specify a name for the project, we chose Methylation Tutorial, using the Save File dialog
- Select Save to save the project
Saving the project saves the identity and child-parent relationships of all spreadsheets displayed in the spreadsheet tree. This allows us to open all relevant spreadsheets for our analysis by selecting the project file.
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