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 [1].

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.

• Define and add comparison, then click Finish.

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.

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

Reference

1. Fisher, R. A. (1935). The Design of Experiments. Edinburgh: Oliver and Boyd. (Established ANOVA within the broader framework of experimental design.)