I have a quick question about the design parameter for DESeq2 analysis
I have an experiment where I have 6 individual animals and the following timepoints: Day 0 (baseline and infection date), Day 1, Day 3, Day 7, Day 10, Day 14. Each animal had a sample drawn on every timepoint and RNAseq run for each timepoint in triplicates.
I am measuring gene changes from Day 0 to each of the corresponding timepoints.
For design I have been just using
design = ~ timepoint
since there are no treatments, just the infection date and subsequent measurements. Would this be correct? The animals were all housed together and were matched by age, weight, and I believe similar genotype.