Figure 2

Yeast dataset: Log-fold-change vs. GC-content. Stratified boxplots of count log-ratio vs. GC-content, after FQ between-lane normalization. Panel (a): Same culture/library preparation, YPD Y1 lanes from flow-cells 428R1 vs. 4328B. Panel (b): Different cultures/library preparations, YPD Y1 lane vs. Y2 lane from flow-cell 428R1. The GC-content effect is the same for the two lanes assaying the same culture/library preparation, so that fold-change estimates do not vary with GC-content. By contrast, the GC-content effect differs between cultures/library preparations and confounds fold-change estimation.