I have RNA-Seq data from time point experiments: T0 and T1, each with 3 replicates for no-treatment (condition1) and with-treatment (condition2). That is, 3 replicates, each, under T0 and T1 for no-treatment and 3 replicates, each, under T0 and T1 for with-treatment.
Type/TimePoints T0 T1 Control 3 Rep 3 Rep Treatment 3 Rep 3 Rep
Question: Is the ratio of gene expression between T0 and T1 in control (no-treatment) significantly different from ratio of gene expression between T0 and T1 in treatment? To rephrase, Is the differential expression I observe between T0 and T1 in treatment solely due to treatment (which can be concluded by taking into consideration the expression at T0 and T1 in control)?
Now, normally in edgeR, one could find out differential expression between control and treatment with replicates. Meaning there are no 2 different time points amongst this comparison. So is this possible using edgeR (or DESeq or BaySeq for that matter)?