Question: Regarding dispersion estimation of RNA-seq data by edgeR software
gravatar for seta
2.6 years ago by
seta1.1k wrote:

Hi all,

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 enter image description here. 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?


edger dispersion estimation • 1.1k views
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