I am new to DESeq2 analysis. I have RNASeq raw count data from three different time points namely 0h, 10h, 2d. Every time point has triplicates for Control samples, Treatment-A, TreatmentB, TreatmentC. All I want to find is the differential expressed genes between Treated against Control samples(Treatment-A vs Control; Treatment-B vs Control; Treatment-C vs Control) for every time point. Now I would like to know whether , I should load raw counts from all the samples together in every time point into R and compute diff. expression analysis OR load the raw counts of particular time point(i.e. Control_0h, Treatment-A, Treatment-B and Treatment-C) at a time and perform differential gene expression analysis.
Can anyone guide me. Thanks in advance.