The Impact of Normalization Methods on RNA-Seq Data Analysis

Figure 2

Diagnostic plots for the AML data set. Besides the five normalization methods, raw data (RD) were also included in the plots as a benchmark. (a) presents calculated normalization factor values across the samples by each method. The samples are ordered by the minimum values of normalization factors. (b) shows 95% confidence intervals for the mean of the percentages of classification errors calculated for each method based on five selected classifiers. (c) shows the numbers of common DE genes across each pair of normalization methods. The size and shading of the circles represent the average percentage value of common genes between each pair of methods. (d) presents the results of clustering of the normalization methods based on 20 common DE genes found by each of these methods. A dendrogram was created with hierarchical clustering based on Ward’s method.

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