Figure 1
Outline of TbT normalization strategy. Left panel: M-A plot for negative binomially distributed simulation data from Ref. [21], after scaling for RPM mapped reads in each sample. Magenta and black dots indicate DEGs (20% of all genes; PDEG = 20%) and non-DEGs (80%), respectively. 90% of all DEGs is four-fold higher in Sample A than B (PA = 90%). Each dot represents a gene. Right panel: same plot but colored differently. TbT estimates 16.8% of PDEG using this data. Gray dots indicate genes estimated as non-DEGs by step 2 in TbT. Note that the median log-ratio for true non-DEGs when data normalization is performed using the TbT normalization factors (0.045) is closer to zero than that using the TMM normalization factors (0.170).