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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 anova-1way_autosomal (autosomal) as the source spreadsheet from the left-hand panel
- Select LCLs vs. B cells from the Contrast: find genes that change between two categories section of the ANOVA Streamlined tab of the List Manager dialog
- Set Fold change > to 20
- Set OR Fold change < to -20
- Set p-value with FDR to 0.005
- Set file name as LCLs vs. B cells
- Leave the rest of the option set to defaults (Figure 1)
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- Select Create
- 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 (Figure 2).
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