HI! I have a question, about design matrix in Deseq2, when I don't have any control or conditions. But same sample at different time points for differential expression analysis . I want to do differential expression between different time points. How I should define my Design ?
design(dds) <- ~Time dds <- DESeq(dds, test="LRT") res <- results(dds)
Also, in another case if I have 3 biological replicates for each time point [no treatment/condition] and want to analyse across time points . It should be like:
design(dds) <- ~replicates + time dds <- DESeq(dds, reduced=~replicates, test="LRT") res <- results(dds)
Is it correct way?
I was trying to take a look o another question, but in that case they have conditions.