> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/detect-differential-methylation.md).

# Detect differential methylation

The Detect Differential Methylation task enables users to perform differential test on methylation array data and Illumina 5-base DNA Prep data. The task converts Beta-values to M-values and uses these to perform [ANOVA differential expression analysis](/icm/analyses/analysis-functionality/task-menu/statistics/differential-analysis/anova-limma-trend-limma-voom.md).

## Running Detect Differential Methylation

* Click to select a methylation data node with beta values.
  * For methylation array: select **Methylation beta** data node.
  * For Illumina 5-base DNA Prep: select **5-base methylation** data node or **Get Regional Methylation** data node.
* Select **Methylation analysis** from context-sensitive menu, select **Detect Differential Methylation**.
* Select a **factor** for analysis, click **Next**.

<figure><img src="/files/iZk75Zf1TPHNefnZ9Dpc" alt=""><figcaption></figcaption></figure>

* Define and **add comparison**, then click **Finish**.

<figure><img src="/files/BvtKI9E7DCQS25RsQTsu" alt="" width="407"><figcaption></figcaption></figure>

## Detect Differential Methylation output

When completed, double-click on the output data node to open task report. Each row in the report table is a probe or methylation feature being tested. The table is sorted by p-values by default. Significance such as P-value and FDR step up are computed from the M-values. The LSMeans of the groups and the Difference are computed from the Beta-values.

Click the **Optional columns** button to add more column data. For array data, annotation from the Illumina manifest file can be selected from the Optional columns.

Click **Volcano icon** next to the comparison name, and icons buttons in **View** columns to open visualizations and additional details on the results.

<figure><img src="/files/TONhTPiRwFszB2vchyQV" alt=""><figcaption></figcaption></figure>

The table can be exported by clicking **Download** button on the top left corner of the table.


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