2.8.1 Differential expression analysis
DESeq2 (v1.30.1) (Love et al. , 2014) using the Wald test was used to compare gene expression between current-day and elevated CO2 conditions for the CNS and eyes separately. Genes with an adjusted p-value (padj, Benjamini-Hochberg method) < 0.05 were reported as differentially expressed (DE). Log2fold change estimates were shrunk with the ashr method (Stephens, 2016) to increase their accuracy.