Skip to main content

Table 1 Benchmarking of UMtools on sex chromosome- and SNP-targeting probes

From: Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications

Tool Scale Purpose
U/M plot Targeted Cluster visualization
bGMM Targeted Cluster assignment for a target number of clusters
BC(CV) Epigenome-wide Ambivalence in noise-to-signal ratio detection
corMZ(CV) Epigenome-wide Genetic control for noise-to-signal ratio
K-caller Epigenome-wide Cluster counting
Markers ChrY ChrXinact ChrXhypermeth + escape SNP probes
# probes 266 3,981 3,028 65
Expected K 2 2 1 (large n) 3
Probe failure in females Yes No No No
(K = 2 or 3)
Twin cluster assignment agreement 0.994 0.991 0.479a 0.997
BC(CVlogT) and corMZ(CV) Genetics-related probe failure 0.951 0.001 0.001 0.000
K-calling Correct # clusters predicted 0.977 0.902 0.999 1.000
  1. a Full separation between males and females is not observed in a large cohort as E-risk (Fig. 1D); it can be seen though in smaller datasets (Additional file 1: Fig S2A) that are not so strongly affected by batch effects