> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-troubleshooting-list/000008918.md).
# How to Determine the Sex of Samples in a GenomeStudio Methylation Project
This article describes two commonly used methods for determining the sex of samples in a GenomeStudio Methylation project and provides step-by-step instructions for each approach.
The methods described assume a working knowledge of the [GenomeStudio Methylation Module](https://emea.support.illumina.com/downloads/genomestudio-2011-1-user-guides.html) and the analysis of data generated from Infinium Methylation Arrays, such as the MethylationEPIC v2 array, or custom methylation arrays that contains a significant number of Y chromosome markers.
These approaches also assume that the project contains a mixture of male and female samples.
**Methods for Determining the Sex of Samples in a GenomeStudio Methylation Project** 1. Filter the Sample Methylation Profile for Y-chromosome markers.\
1\. In the Sample Methylation Profile table, select the "Filter" button (Figure 1).
**Figure 1.** Sample Methylation Profile table in GenomeStudio Methylation Module.
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2. In the subsequent pop-up window, create a filter with the condition "CHR = Y" to display markers located on the Y chromosome (Figure 2).
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**Figure 2.** Filter Settings window for the Sample Methylation Profile table in GenomeStudio.
**Important Note:** If the data was analyzed using the manifest EPIC-8v2-0\_A1.bpm, the chromosome designations differ from those used in other MethylationEPIC manifests by including the prefix "chr" (Figure 3).
\*\*Figure 3.\*\*Example of the CHR column displayed in a GenomeStudio Methlylation project created using the manifest file EPIC-8v2-0\_A1.bpm.
In this case, the value input for the chromosome must include this prefix. Therefore, the filter must be set to "Chr = chrY", otherwise, GenomeStudio will not correctly recognize the chromosome and the filter will not return the expected results (Figure 4).
**Figure 4.** Filter Settings for a GenomeStudio Methylation project using the EPIC-8v2-0\_A1.bpm manifest.
1.
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3. Select "OK". The markers displayed in the Sample Methylation Profile table will now be limited to Y-chromosome markers only (Figure 5).
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**Figure 5.** Sample Methylation Profile table filtered for Y chromosome using the manifest EPIC-8v2-0\_A1.bpm.
2. Inspect the Y-chromosome intensity values for the samples in the Sample Methylation Profile table.
1. In the Sample Methylation Profile table, select the Box plot button (Figure 6).
**Figure 6.** Box plot button in the Sample Methylation Profile table.
1. 2. In the subsequent pop-up window, select the "Intensity" subcolumn. Female samples generally show near-background intensities, while male samples exhibit noticeably higher intensity values (Figure 7).
**Figure 7.** Y-chromosome Intensity Box plot of Y chromosomes.
**Alternative method**
The following publication describes an alternate method utilizing the beta values from the X chromosome to determine sex from Infinium Methylation array 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.](https://pmc.ncbi.nlm.nih.gov/articles/PMC8240370/) BMC Genomics. 2021 Jun 28;22(1):484. doi: 10.1186/s12864-021-07675-2. PMID: 34182928; PMCID: PMC8240370.
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #8918), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008918%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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