Multidimensional scaling plots of M values by batch for all normalisation methods. Multidimensional scaling plots for raw (A), quantile normalisation (B), BMIQ (C), SWAN (D), FunNorm (E), Dasen (F), noob (G), stratified QN (H), raw with ComBat correction (I) and stratified QN with ComBat correction (J). For each plot, the 1000 most variable probes were selected. Batches are numbered and coloured, with clustering by batch clearly seen in the raw data (A) and removed to varying degrees with different normalisation methods. ComBat correction following stratified QN provides optimal batch correction removal as the samples no longer cluster according to batch. (PDF 559Â kb)