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.

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.

Choose one of the normalization method: NOOB, Functional, 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:

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