> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/icm/analyses/analysis-functionality/task-menu/pre-analysis-tools/generate-beta-value.md).

# Generate beta value

This task is only available on imported microarray methylation data node. The microarray methylation node contains probe methylated/unmethylated signal intensities on green/red channels on each sample. Beta value needs to be generated for each probe in each sample, which represents the ratio of methylation at a CpG site \[1]: methylated intensity divided by the total intensity. The range of beta value is between 0 and 1.

<div align="left"><figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-bdbbbe6e72754b9f57be9cdedf579a247e5b8115%2Fbeta%20(1).png?alt=media" alt="" width="563"><figcaption></figcaption></figure></div>

Information about which array type needs to be retrieved from the manifest file, select the chip name from the drop-down list.

During the conversion, probe filtering can be performed. Depends on the study, probes on X/Y chromosomes can be filtered out to reduce the data size.

When check *Exclude probes using detection p-value* option, specify the p-value cutoff and number of samples.

<div align="left"><figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-d2cbce86d462d5ceb0cfd5f01c7a49f3155b6a08%2Ffilterbeta.png?alt=media" alt="" width="563"><figcaption></figcaption></figure></div>

Choose one of the normalization method:[ NOOB](http://bioconductor.org/packages/release/bioc/html/minfi.html), [Functional](https://bioconductor.org/packages/release/bioc/html/minfi.html), or None and corresponding parameter settings.

Click **Finish** to run the task, it will generate *Methylation beta data node*.

In the Advanced options configure dialog, there are options to output more values of each probe besides beta value:

<div align="left"><figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-d7fa60252ddf292de17ce150854d572b92d0f53a%2Fbetaadv.png?alt=media" alt="" width="483"><figcaption></figcaption></figure></div>

Each check option will result a .tsv file. The extra information can only be downloaded. After the task is finished, click on the Microarray methylation task (rectangle) and choose Task details > View output files to retrieve the file(s).

## Reference

1. <https://bioconductor.org/packages/release/bioc/html/minfi.html>


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