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.