A systematic evaluation of normalization methods and probe replicability using infinium EPIC methylation data

Clinical Epigenetics

Table 1 Absolute beta-value (|∆β|) differences for all replicate samples

	Q1	Q2 (Median)	Q3	Upper Whisker	\|Δβ\| > 0.05 (%)	\|Δβ\| > 0.10 (%)	Type
Raw 1	0.00734	0.01627	0.02931	0.06226	6.50	0.30	–	–
BMIQ1	0.00578	0.01348	0.02627	0.05699	5.74	0.33	Quantile	Within-array
SWAN 1	0.00588	0.01286	0.02357	0.05009	4.27	0.30	Quantile	Within-array
Illumina 1	0.00554	0.01206	0.02167	0.04587	2.86	0.21	Correction*	Within-array
Quantile 1	0.00523	0.01164	0.02148	0.04587	3.63	0.43	Quantile	Between-array
Noob 1	0.00379	0.00911	0.01822	0.03987	2.47	0.21	Correction*	Within-array
Funnorm 1	0.00362	0.00890	0.01792	0.03936	2.67	0.30	Mixed	Between-array
SeSAMe 1	0.00342	0.00840	0.01763	0.03895	2.49	0.21	Correction*	Within-array
Noob + BMIQ 1	0.00333	0.00829	0.01771	0.03928	2.75	0.25	Mixed	Within-array
SeSAMe 2	0.00333	0.00815	0.01709	0.03773	1.97	0.10	Correction*	Within-array

ISSN: 1868-7083