I have 8 RNA-Seq samples. Among them 4 are controls and other 4 are treatment. I'm interested in doing differential analysis with edgeR. Following is the column data.
Samples Type Sample1 Control Sample2 Control Sample5 Control Sample6 Control Sample7 Treatment Sample8 Treatment Sample3 Treatment Sample4 Treatment
Among the above table Sample1, Sample2 [Controls] and Sample3, Sample4 [Treatment] are done on one day and Sample5, Sample6 [Controls] and Sample7, Sample8 [Treatment] are done on other day.
As you see the replicates were not processed together, there is the batch effect. In this way how I can create the design matrix in edgeR for differential analysis.