Fig. 3

Consistency in differential expression signal across normalization methods. a Correlation heatmap showing concordance (Spearman rho) among ranks of differentially expressed genes using the four normalization methods (n = 7276). Genes were ranked by raw t-test p-values. b Correlation heatmap showing concordance (Spearman rho) among fold-change of differentially expressed genes using the four normalization methods (n = 7276). c Hierarchical Clustering of top 200 differentially expressed genes with uncorrected data shows strong clustering of samples by study rather than by phenotype. d Hierarchical Clustering of top 200 differentially expressed genes with QN + SVA (Quantile Normalized + SVA) corrected data clusters by epithelial and mesenchymal phenotype