Fig. 2

Distribution of the median δRPKM values across all genes. For a given dataset analysis and for a given gene, the median value m of all its δRPKM is plotted (diamonds). A standard deviation of all the gene median values (s_m) is then used to threshold (set as 2 ∗ s_m by default) the significance of differential presence between the two groups of samples. Genes with a median δRPKM value m >  = 2 ∗ s_m are considered as differentially present in the reference group. The red dotted line corresponds to 2 ∗ s_m. The grey dotted line corresponds to the Median Absolute Deviation (MAD). This summary plot can be produced when running the method deltaRpkm::median_plot. A dataset of size N = 51 from Listeria monocytogenes (genome size ~ 3 Mb for ~ 3 K genes) was used for the analysis represented in the figure, see [1].