How to obtain Unmethylated and Methylated signal in GenomeStudio for each CpG in MethylationEPIC Array

For Methylation arrays, the Beta value is calculated as: Signal B/(Signal A + Signal B + 100)

where Signal A = Unmethylated and Signal B = Methylated

To obtain Signal A (Unmethylated) and Signal B (Methylated) values in GenomeStudio 2011.1 software in the Methylation Module:

1. Under the Sample Methylation Profile table, select the "Column Chooser" icon

1. The "Column Chooser" window pops up. Under Hidden Subcolumns on the right side, highlight "Signal_A" and "Signal_B".

Then click the "<=Show" button so that these values appear under Displayed Subcolumns.

1. The "Signal_A" and "Signal_B" columns should now appear as a subcolumn under each sample. Each row (cg probe) will have a corresponding Signal_A and Signal_B for each sample. Intensity = Signal_A + Signal_B

External Links: GenomeStudio Methylation Module v1.8 User Guide Recorded Webinar: Infinium Methylation: Introduction to GenomeStudio Analysis and BeadArray Controls Reporter

For any feedback or questions regarding this article (Illumina Knowledge Article #6306), contact Illumina Technical Support [email protected].