Fig. 7
From: “Gap hunting” to characterize clustered probe signals in Illumina methylation array data
Examples of probes with a polymorphism that do not result in a gap signal. Most probes that overlap with SEED SNPs are not classified as gap signals. These probes can generally be grouped into 3 categories: a In SEED, cg14613402 overlaps with a C/T SNP at the interrogated C site and displays a negative correlation with dosage of the T allele. However, a discrete difference in the groups is not achieved. b cg15012523 overlaps with a C/T SNP at the interrogated C site and also displays a negative correlation with dosage of the T allele. Here, a discrete difference does existence between the TT genotype and others and thus would be identified via gap hunting; it would be classified as an outlier-driven signal with the default algorithm arguments, however (see “Methods” section). c cg15283160 overlaps with a C/T SNP at the interrogated C site but displays no variability in beta value