Figure 4.6: Histogram of the raw per-gene p-values from the moderated t-test . The horizontal ``floor'' of values in this plot corresponds to the large number of features whose target genes are not differentially expressed. The sharp peak at p<0.001 corresponds to differentially expressed genes. The shape of this histogram can be used to assess an experiment and its analysis: if the peak on the left is missing, this indicates lack of power of the experiment or of the analysis to detect differentially expressed genes. If the remainder of the distribution is not fairly uniform, this can indicate overdispersion and/or a strong interfering effect of another variable, for example, an unintended batch effect.