Gene expression fold change in the TDP-43 deletion vs wild type genes (Chiang dataset). Gene expression fold change is plotted against the average tag counts (x-axis in base-10 log; y-axis in base-2 log). The 300 most significantly differentially expressed genes by p-value are depicted by squares (t-test), diamonds (beta-binomial distribution), and triangles (binomial distribution). Black circles represent genes not among the top 300 in any methods. The green and purple boxes and lines indicate the median for RPKM and peak of proportional normalization. The data were from the average of three deletion and two wild type experiments.
Cai et al. BMC Bioinformatics 2012 13(Suppl 13):S5 doi:10.1186/1471-2105-13-S13-S5