# 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

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-aa7c7111e599a450e06978d90beee5a3ced49f9e%2Fimage1.jpg?alt=media)

2. 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.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-1afad5056c08306ce9dd0cf78373c79b935a7541%2Fimage2.jpg?alt=media)

3. 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\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-ae6b8e064b7a592d0ad9aa123fa3f97fdcc56a78%2Fimage3.png?alt=media)

**External Links:**\
[GenomeStudio Methylation Module v1.8 User Guide](https://support.illumina.com/downloads/genomestudio-2011-1-user-guides.html)\
Recorded Webinar: [Infinium Methylation: Introduction to GenomeStudio Analysis and BeadArray Controls Reporter](https://www.youtube.com/embed/tuY7DEMSolE?autoplay=1\&rel=0)

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                   |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #6306), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006306%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |