I am interested in using DESeq2 to analyze a bulk RNA-seq dataset with one factor and 12 levels (control and treatments), and 4 biological replicates per level. I was wondering how using one or multiple input sample tables would influence the genes that are found to be differentially expressed. For example, 1) I could provide a single table of sample information and then look at the possible pairwise contrasts between control and treatment levels. Alternatively, 2) I could provide multiple sample tables, one for each control-treatment pair. Will there be major differences in the genes found to be differentially expressed between either approach for the same control-treatment comparison?
I would be grateful for any insights/suggestions.