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An alternative metric for measurement of methlyation levels are M-values. β-values can be easily converted to M-values using the following equation:

M-value = log2( β / (1 - β))

An M-value close to 0 for a CpG site indicates a similar intensity between the methylated and unmethylated probes, which means the CpG site is about half-methylated. Positive M-values mean that more molecules are methylated than unmethylated, while negative M-values mean that more molecules are unmethylated than methylated.  As discussed by Du and colleagues, the β-value has a more intuitive biological interpretation, but the M-value is more statistically valid for the differential analysis of methylation levels.

Because we are performing differential methylation analysis, we need to convert our data to from β-values to M-values.

• Select Convert Beta Value to M Value from the Import section of the Illumina BeadArray Methylation workflow

The original data (β-values) will be overwritten.

• Select (Image Removed) from the icon bar to save the current spreadsheet 

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