I have two samples (control and treatment) with 3 biological replicates. For differential expression analysis, I tried dispersion estimation by edgeR with the commands of
y <- estimateDisp(y, design, robust=TRUE) and
plotBCV(y), which gave me the below picture . However when I used the command of
y <- estimateCommonDisp(y, design, verbose=TRUE), it returned me (Disp = 0.608 , BCV = 0.78), but the common dispersion is something around 0.2 (red line) in the graph picture, am I right or wrong? Could you please tell me why there is such a difference and what is the right common dispersion?
I read a lot on the net, but the Trended and Tagwise dispersions are not still clear for me. Please kindly tell me what do they show us?