Resolution:
## Figure 6.
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 |