```r
ddsFull <- DESeqDataSet(se, design = ~ patient + treatment)
ddsCollapsed <-
    collapseReplicates(ddsFull, groupby = ddsFull$sample, 
                       run = ddsFull$run)
dds <- ddsCollapsed[, ddsCollapsed$time == "48h"]
dds$time <- droplevels(dds$time)
dds$treatment <- relevel(dds$treatment, "Control")
```