How does NimbleGen perform analysis on DNA methylation data?
After scaled log2 ratio data is generated a modified ACME algorithm (Method Enzymol. 2006; 411:270-282) is employed where a fixed-length window is slid along the length of each chromosome, testing at each probe using a one-sided Kolmogorov-Smirnov (KS) test whether the surrounding window is enriched for high-intensity probes relative to the rest of the array. Each probe has a corresponding p-value score (-log10) and a threshold is set to select regions that are enriched (i.e. methylated) in the test sample. If you are a DNA Methylation array customer and are stil using NimbleScan 2.3 you will need to download the ACME plug-in by clicking here.
