How to back calculate the differential p value from Diffscore with Genomestudio Methylation Module

How to back-calculate p-value of the differential (differential p-value) from Diffscore from the Genomestudio Methylation Module?

When a Differential Analysis is run in GenomeStudio Methylation Module, the software provides a DiffScore for each group's beta values. The DiffScore is a log transformation of the p-value of the differential, or differential p-value, which in turn reflects the likelihood that a given group's β value for a specific CpG assay is within error of a reference group's β value for that same CpG assay. However, the software does not present the actual p-value from which the DiffScore is derived, ie, there is not an option to display the differential p-value in the software. The differential p-value can be back calculated from a given Diffscore, using the formula for Diffscore.

Where:

• 10 is a multiplier to increase the dimension of the Diffscore.

• sgn (β(conditional) - β(reference)) yields a positive or a negative sign to indicate whether the β value of the experimental group is higher or lower than the reference group.

• p is the differential p-value.

The following formula derives p from the Diffscore using the absolute value of the Diffscore, because it does not matter whether the experimental or reference β is higher or lower:

|Diffscore| = -10*log10(p)

-(|Diffscore|/10)= log10(p)

p=10-(|diffscore|/10)

So, the differential p-value is 10 to the power of the negative of the quantity of absolute value of the Diffscore divided by 10.

For example, when entering the following Diffscores into the formula, the corresponding Diffscores result.

• Diffscore = 13 Differential p-value = 0.05

• Diffscore = 20 Differential p-value = 0.01

• Diffscore = 30 Differential p-value = 0.001

Reference: GenomeStudio Methylation Module v1.8 User Guide: see page 51 for the Diffscore formula and for definition of p-value.

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