Fig. 3
From: eUTOPIA: solUTion for Omics data PreprocessIng and Analysis
Normalization summary. Box plots (a; b), Density plots (c, d), and Mean-Difference plots (E, F) report expression values before and after normalization. The Box plots (a, b) report the distribution of expression values in each array. The Density plots (c, d) report the density distribution of the expression in individual color channels of each array. The expression intensity is plotted on the x-axis and the density values on the y-axis. The Mean-Difference plots (MD plot) (e, f) report agreement of the expression values between the individual channels of the array. The M-values (log-2 expression ratios) are plotted against the A-values (average log-2 expression values) as scatterplots. The A-values are plotted on the x-axis, and the M-values are plotted on the y-axis