Hi all,

I had a question about DESeq2, or a little sanity check.

In my case I'm only interested in comparing how expression differs between conditions at specific time-points. I believe I can do comparisons with combined factors e.g. Responder_Week1 v NonResponder_Week1 - but I can also do LRT for full time-course comparisons? Is there a particular method that would be better suited? I believe that I can get similar results from LRT by using the names - however I think I've confused myself further - so I could use a hand.

#Code I've been using
#Using response to treatment and time-point as the design for DESeq
dds <- DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~response+ time + response:time) 

#Using the time-point as the reducement, which means we are testing the effect of the response?
dds <- DESeq(dds, test = "LRT", reduced = ~time) 

#Get the results, 
results(dds) # However, this will be for all, but we can get a specific comparison by using name and Wald test
results(dds, name = "responseResponder.timeW1", test = "Wald") 
#But then, is this comparing a Non-Responder to Responder at Week 1 or Responder at Week 1 against the Base time-point?

#OR, by combined factors, where condition = e.g. Responder_Week1 
dds <- DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~condition) 

#And now results is simply
results(dds, c("condition","Responder_Week1", "NonResponder_Week1"))

Please do correct me, direct me, or criticise me - I'm only hoping to learn more and do this correctly :)

I hope this makes sense, if there's any confusion please feel free to ask (I am confused myself, hence my reaching out!)