I would like to test differential gene expression in two groups of genotypes using genotypes nested within groups as a random effect. All genotypes measured in 2 treatments.
I understand that I can specify nested effect
dds <- DESeqDataSetFromMatrix(countData, colData, design= ~ treatment + group + group:treatment + group:genotype)
and this will test treatment and group as main effects and their interaction, but will group be tested against genotypes within groups?