Comparison of different normalization models. (a-c) MA plot of H3K27ac peaks in H1 ES cells and K562 cells after normalization by total reads (a), quantile normalization (b) and genome-wide MA plot followed by LOWESS regression (c). The corresponding MA plot based on MAnorm is shown in Supplementary Figure 2a in Additional file 2. (d-g) Scatter plot of log2 expression ratios of target genes between H1 ES cells and K562 cells versus the M values normalized by total reads (d), quantile normalization (e), genome-wide MA plot followed by LOWESS normalization (f), and MAnorm (g). The color bar represents the density of dots in the scatter plot and purple dots represent the outliers separated from the others. (h) Distribution of M values for each normalization method and distribution of log2 expression ratios of non-differentially expressed target genes (fold-change < 1.5). T-statistics and P-values calculated based on one sample Students' t-test comparing to 0 for each normalization method were as follows: MAnorm, t-statistic = -0.55 and P = 0.58 by t-test; total reads normalization, t-statistic = -88 and P < 1E-100; quantile normalization, t-statistic = -140 and P < 1E-100; genome-wide MA, t-statistic = 24 and P < 1E-100. For non-differentially expressed target genes, t-statistic = -0.76 and P = 0.45.
Shao et al. Genome Biology 2012 13:R16 doi:10.1186/gb-2012-13-3-r16