I am analysing RNASeq data from human tissue samples for disease and normal patients. I have in total 3 types of data: disease1 (n=12), disease2 (n=10) and normal (n=20). Some of my data were sequenced later and I see a clear batch effect. I am using EdgeR and design matrix is: design<-model.matrix(~SeqTag + DiseaseTypes)
My BCV value is 0.2 which suggests around 20% variation between replicates. But using tagwise dispersion no differentially expressed genes were predicted at 0.05/0.1 pvalue for any type. My tagwise dispersion range is 0 to 4.4.
If I used only common dispersion then I am getting around 50 DEgenes. I also see more than 4000 genes are differntially expressed between two batches.
My questions are
(1) Can I used common dispersion only as it is not recommended
(2) What could be the reason that no DE gene predicted although BCV is around 0.2 ?
Any other suggestion. Thanks in advance.