I have a dataset from 4 patients at 3 timepoints. This is the design formula:
dds <- DESeqDataSetFromMatrix(cluster3_counts, colData = metadata_3, design = ~ orig.ident + timepoint)
First question: I tried two design formula, one is
design = ~ orig.ident + timepoint and the other is
design = ~ timepoint, but from PCA plot, they looked the same.
And then I run DESeq2:
dds_lrt <- DESeq(dds, test = "LRT", reduced = ~ orig.ident)
Second question: how to extract the results for all comparisons, like timepoint 2 vs. timepoint 1?
Although I read the tutorial ?results, there are no such an example and I am still confused.