Fig. 3

Density distribution of β values. Density plot and probe distribution of β values for raw pre-normalisation data (a, b), after stratified QN (c, d) and with stratified QN and ComBat batch correction (e, f). For density plots (a, c, e), a single line represents a sample, with samples coloured by batch. A clear batch effect is present in a, lessened in c and removed in e. For the probe distribution (b, d, f), one sample has been chosen with the red dashed line indicating type I probe distribution, the blue dashed line type II and the solid black line the combined probe distribution. The probe type distribution is also improved after normalisation, as types I and II are more closely aligned in d and f compared to b