Comparing the overall expression of detected biological RNA categories within individual samples illustrates consistency among nonalcoholics and alcoholics (Fig. 11.2). Alternatively, any possible discrepancies that may need special consideration in downstream analyses may also be revealed through this type of comparison. The global expression level of transcriptome elements is stable among individuals from alcoholics and matched controls (Fig. 11.3A), and is also similar in terms of sensitivity, determined through the number of counts per million (CPM) mapped reads over varying levels of stringency (Fig. 11.3B). General agreement across the samples indicates the absence of a potential batch effect or outliers within the examined cohort. Sequencing depth, based on reliably and unambiguously mapped reads, is nearly uniform across controls and alcoholics for all of the biological units (Fig. 11.4A), as well as for only protein-coding transcripts (Fig. 11.4B). Although increased sequencing depth could improve expression estimates, continuity between specimens suggests reliable biotype measurements for comparing alcoholic and nonalcoholic subjects. Importantly, lack of overall expression differences in proportion to disease state does not exclude finding potential differences in discrete RNA molecules, which may be important players in the development of alcohol use disorder.
