How to obtain Unmethylated and Methylated signal in GenomeStudio for each CpG in the Infinium MethylationEPIC Array
For Illumina Methylation arrays, the Beta value is used as a quantitative measure of DNA methylation at a given CpG site. It represents the proportion of methylated signal relative to the total signal intensity and is calculated using the following formula:
Figure 1. Formula for calculating the Beta value.
where:
Signal A corresponds to the unmethylated intensity value, and
Signal B corresponds to the methylated intensity value.
The constant value of 100 is included to stabilize Beta values, particularly at low signal intensities.
To obtain the Signal_A (Unmethylated) and Signal_B (Methylated) values in GenomeStudio v2011.1, users must access these data within the Methylation Module.
The following steps outline how to view and export these signal intensities for downstream analysis.
Under the Sample Methylation Profile table, select the "Column Chooser" icon
Figure 2. Column Chooser icon in the Sample Methylation Profile table.
The "Column Chooser" window pops up. Under Hidden Subcolumns on the right side, highlight "Signal_A" and "Signal_B". Click the "<=Show" button.
Figure 3. Selection of Signal_A and Signal_B subcolumns within the Sample Methylation Profile Column Chooser.
Signal_A and Signal_B appear in the Displayed Subcolumns.
Figure 4. Addition of Signal_A and Signal_B to the Displayed Subcolumns section in the Column Chooser.
The Signal_A and Signal_B columns appear as subcolumns under each sample, with corresponding values for each cg probe. The total intensity is calculated as:
Intensity = Signal_A + Signal_B.
Figure 5. Display of Signal A and Signal B columns in the Sample Methylation Profile table after column customization.
Additional references:
For any feedback or questions regarding this article (Illumina Knowledge Article #6306), contact Illumina Technical Support techsupport@illumina.com.
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