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.

DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points

If you have replicates that track across time you would use ~rep + time for the full model and ~rep for the reduced model. If you don't have replicates that track across time, you would use ~time for the full model and ~1 for the reduced model.