How to calculate the P value of illumina DNA methylation chip probe

In this issue, the editor will bring you about how to calculate the P value of illumina's DNA methylation chip probe. The article is rich in content and analyzes and describes for you from a professional point of view. I hope you can get something after reading this article.

Illumina's DNA methylation chip has a built-in control probe for detection, noise reduction, normalization and other uses.

Taking 450K as an example, there are 15 types of control probes, each of which has different uses.

> unique (IlluminaHumanMethylation450kmanifest@data$TypeControl [[2]]) [1] "STAINING", "EXTENSION" [3], "HYBRIDIZATION", "TARGET REMOVAL" [5], "BISULFITE CONVERSION I", "BISULFITE CONVERSION II" [7], "SPECIFICITY I", "SPECIFICITY II" [9] "NON-POLYMORPHIC"NEGATIVE" [11] "RESTORATION"NORM_A" [13] "NORM_G"NORM_C" [15] "NORM_T"

Among these control probes, the NEGATIVE probe is used to calculate the P value of the probe.

The process of calculating the probe P value in minfi is as follows:

P value of probe = 1-P (intensity)

Assuming that the signal strength of the probe obeys the normal distribution, the expectation and variance of the normal distribution should be calculated first.

Because the technical principles of type I probe and II type probe are different, the two probes are calculated separately.

Firstly, according to the signal strength of negative probe, the mean and variance of red and green channels are calculated respectively.

# get the IDcontrolIdx of negative probe