# A quick visualization method to help determine the sex of given samples in a GenomeStudio Methylation project
The following method assumes a working knowledge of the GenomeStudio Methylation Module, and the analysis of data from an Infinium Methylation Array, such as Methylation450K, MethylationEPIC, or MethylationEPIC v2, or a custom methylation array that contains a significant number of markers being assayed that are on the Y chromosome. It also assumes that there is a mixture of samples with regard to sex.
Step 1: filter the sample methylation profile for Y chromosome markers, then compare the intensities for the samples across the project.
* In the sample Methylation Profile table, click on the "Filter" button\
* In the subsequent pop-up window, create a filter: "CHR = Y"\
* IMPORTANT NOTE - If your data was analyzed using the manifest "EPIC-8v2-0\_A1.bpm", the chromosome designations are unlike all other MethylationEPIC manifests, in that they include a prefix "chr".\
In this case, the Value input for the chromosome must include this prefix, i.e. the filter must read "Chr = chrY", otherwise the filter will not recognize the chromosome designation correctly.\
* Click on "OK". The displayed markers in the Sample Methylation Profile table will now consist only of Y-chromosome markers\
Step 2 - inspect the Y-chromosome intensity values for the samples in the Sample Methylation Profile table.
* In the Sample Methylation Profile, click on the Box plot button\
* In the subsequent pop-up window, select the "Intensity" sub column. Females will have near background intensities, while males will show elevated intensity boxes.\
**Alternative method**
The following publication describes an alternate method utilizing the beta values from the X chromosome to determine sex from Infinium Methylation data:
Wang Y, Hannon E, Grant OA, Gorrie-Stone TJ, Kumari M, Mill J, Zhai X, McDonald-Maier KD, Schalkwyk LC. DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy. BMC Genomics. 2021 Jun 28;22(1):484. doi: 10.1186/s12864-021-07675-2. PMID: 34182928; PMCID: PMC8240370.
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