Beadchip Array Design - sups-k/methylation GitHub Wiki

For the 450k microarray, each sample is measured on a single array, in two different color channels (red and green). Each array measures roughly 450,000 CpG positions. Each CpG is associated with two measurements: a methylated measurement and an “un”-methylated measurement. These two values can be measured in one of two ways: using a “Type I” design or a “Type II design”. CpGs measured using a Type I design are measured using a single color, with two different probes in the same color channel providing the methylated and the unmethylated measurements. CpGs measured using a Type II design are measured using a single probe, and two different colors provide the methylated and the unmethylated measurements.

Practically, this implies that on this array there is not a one-to-one correspondence between probes and CpG positions. We have therefore tried to be precise about this and we refer to a “locus” (or “CpG”) when we refer to a single-base genomic locus (the actual CpG position given by the probe name "cg"), and we differentiate this from a “probe” (which is just the probe address from the manifest file).

Differences in DNA methylation between samples can either be at a single CpG which is called a differentially methylated position (DMP), or at a regional level which is called a differentially methylated region (DMR).

Physically, each sample is measured on a single “array”. For the 450k design, there are 12 arrays on a single physical “slide” (organized in a 6 by 2 grid). Slides are organized into “plates” containing at most 8 slides (96 arrays). The EPIC array has 8 arrays per slide and 64 arrays per plate.

Reference: https://bioconductor.org/packages/3.11/bioc/vignettes/minfi/inst/doc/minfi.html#31_advanced_notes_on_reading_data , Section 1.2