Figure 11.

Reproducibility of differential expression (DE) between microarray and RNA-seq. Raw P-values of differential expression in − log10 scale for DE genes called at 10% FDR by both, limma (y-axis), from microarray data, and the other compared DE detection method applied on RNA-seq data (x-axis). A regression line is depicted in red. On the bottom-right corner of each panel, ρ indicates the Pearson correlation whereas R² and P indicate, respectively, the coefficient of determination and P-value of the test for zero regression coefficient, of the − log10p-values of limma as function of those from the compared RNA-seq method. Only tweeDEseq provides a significant (p<0.05) level of reproducibility between P-values of DE genes reported by both, limma on microarray data and the compared RNA-seq method, attaining also the highest ρ and R² values. Blue dots indicate genes with documented sex-specific expression.