Density distribution of β values and multidimensional scaling plots of M values for replicate samples. Density (A, C, E) and MDS (B, D, F) plots of three replicate sample groups for raw (A, B), stratified QN (C, D) and stratified QN ComBat-corrected (E, F) data. For all plots, samples are coloured by batch 1–3 as labelled. Density plots show the distribution of β values, which become more uniform after stratified QN (C) and stratified QN plus ComBat (E). MDS plots show clustering of the 1000 most variable sites by M value, highlighting the decreasing variance between replicate groups after stratified QN and ComBat (F). (PDF 7387 kb
