We demonstrate the use of the rlog transformation on the RNA-seq dataset of Hammer et al. [26], wherein RNA was sequenced from the dorsal root ganglion of rats that had undergone spinal nerve ligation and controls, at 2 weeks and at 2 months after the ligation. The count matrix for this dataset was downloaded from the ReCount online resource [27]. This dataset offers more subtle differences between conditions than the Bottomly et al. [16] dataset. Figure 5 provides diagnostic plots of the normalized counts under the ordinary logarithm with a pseudocount of 1 and the rlog transformation, showing that the rlog both stabilizes the variance through the range of the mean of counts and helps to find meaningful patterns in the data.
