Scatterplots between replicates. After application of different normalization methods, expression values for the respective replicates at 12 hours are plotted against each other. bg_vsn as well as noBg_vst_rsn display a symmetrical distribution of expression values around the main diagonal (orange line), with bg_vsn exhibiting more scattering values especially obvious in low regions of expression. The scatterplot based on bg_vst_loess is slightly bended towards the upper diagonal based on a bias to higher values in the expression values for Replicate 4. Thus, scores of -2, 1, and 2 are assigned to the scatterplots based on bg_vsn, bg_vst_loess, and noBg_vst_rsn, respectively. For an overview over all methods, see Additional file 6.