I want to ask a question in using DESeq, do I also need to import two conditions each time to do the estimatesizefactor and estimatedispersions? Can I import all conditions (>=3) together, and then do sizefactor and dispersion together, and then use res<-nbinomTest(cds,"cond1","cond2") to select which two conditions I want to compare?
In DESeq document, I see in the chapter "working partially without replicates", it indicates to do estimatesizefactor to new cds, but in the chapter " working without any replicates", I see there don't need to do that. So What is the affection if I do estimatesizefactor with all or partial conditions, since I see the sizeFactor is different.
thanks a lot!