Fig. 3
From: MUREN: a robust and multi-reference approach of RNA-seq transcript normalization
Evaluation of different normalization methods by the truncated transcriptome in THI experiments. A Top panel: densities of log ratios of the truncated transcriptome. After truncation, RLE, UQ, TMM, and Q are disturbed by the truncation/asymmetry; the modes of log ratios’ densities from these methods shift notably towards right. MUREN is resistant against the disturbance and keeps its mode near zero. Bottom panel: densities of log ratios of the untruncated transcriptome. The methods CPM and TPM cannot adjust the modes of densities near zero. B M–A plots of ERCC sequences of selected methods applied to the truncated transcriptome. Compared with Fig. 2, TMM has larger deviations between the estimated and expected log ratios due to the influence of truncation. It cannot normalize the counts as well as it does for the untruncated transcriptome. By comparison, MUREN is resistant against the asymmetric perturbation. See Additional file 1: Fig. S5 for the results of other methods