Yeast dataset: Proportion of DE genes vs. GC-content. Here, a gene is declared DE between the three growth conditions if its nominal unadjusted p-value from the negative binomial LRT is below the threshold of 10-5 (corresponding to a nominal Bonferroni family wise error rate of 0.057 and Benjamini & Hochberg  false discovery rate of 4.22 × 10-5). There is a clear trend towards more detected differential expression at higher GC-content with all within-lane normalization procedures but the full-quantile.
Risso et al. BMC Bioinformatics 2011 12:480 doi:10.1186/1471-2105-12-480