Fig. 2

Length differences between orthologous genes introduce gene expression biases. Relation between length differences and the log2-fold change in the RNA-seq experiment between D. mauritiana and D. simulans using the direct re-annotation of these species as mapping references. Dots represent genes with length difference > 49 bp in these annotations (658 genes). Genes significantly differentially expressed in the presented analysis (padj < 0.05) are shown in red. A negative log2-fold change indicates higher expression in D. mauritiana. A positive length difference indicates that the ortholog of D. mauritiana is longer. The p-value and rho of the Spearman’s rank correlation are indicated on the lower right side of the plots. a Results of DESeq2 without length correction. b Results of DESeq2 applying length normalization factor matrix. c Results of applying RPKM normalization and limma to call differentially expressed genes. d Results of applying voom normalization followed by a length normalization matrix and limma to call differentially expressed genes