This is my first time using the DESeq2 package for RNA-seq analysis. I am analyzing a longitudinal study of three different time points in mice, with three different genotypes of animals - 1 wildtype, 2 mutated. I want to evaluate differential expression as an effect of the different genotypes across each age. For example, I want to evaluate differential expression in the 1 year old mice from each genotype and so on. I am confused on how I should compare expression levels across the genotypes at specific time points, using the code below
ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampletable, directory = directory, design = ~ Age + Genotype
Any help with how to properly use "design" would be greatly appreciated!