Looking to get some advice on the appropriate design / contrast matrix for my analysis please. I have 30 independent samples that have been generated in three batches. Each batch contains 10 samples (5 treated and 5 untreated controls). The treated samples in each batch are from a different time-point - where time-point is an ordinal variable; batch 1 = "short time point", batch 2 = "medium timepoint", batch 3 = "long timepoint".
time <- rep(c("short", "medium", "long"), 10)
treatment <- rep(c(rep("drug",3),rep("control", 3)), 5)
batch <- rep(c("1", "2", "3"), 10)
tibble(treatment, time, batch)
I am looking to identify genes that up- / down-regulated across all time points. Because time point and batch are indistinguishable, I would also like to use the control samples to adjust for any batch effects (assuming all control samples are similar across batches). Any advice greatly appreciated.