Fig. 3

Visualization of the insights obtained from an RLE plot, representing (a) log gene expression distributions for 27 samples (without performing quantile normalization) and (b) relative log gene expression distributions for the same 27 samples. The RLE plot allows to highlight the unwanted variation due to the between-batch variation (cyan versus magenta boxplots) as well as the within-batch variation as suggested by both the difference in location (median further from 0) and spread (higher IQR) of the boxplots. This interpretation is under the often-plausible assumption that expression levels of most genes are unaffected by the biological factors of interest. Source: [32]