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 LCLs vs. B cells (Figure 1)
- 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.
It is best practice to occasionally save the project 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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