Non-symmetric MA-plot (DESeq2)
I performed differential analysis of RNA-Seq using DESeq2 of mouse samples, with different genotype (WT and KO) and diet (CD and HFD). I expecting to have a lot of differential expressed genes (because of strong macroscopy differences), but I found MA plot are non-symmetric (“Raw data” on plots indicate that I don’t shrink data, but of course I used normalized data):
- genotype effect:
- diet effect:
- interaction genotype and diet:
Size factors are between 0.71 and 1.25 (13/15 samples are between 0.91 and 1.15).
Is it “problematic” that MA-plots are not centered on the x-axis? Do you advise me to do other analyzes to better understand it?
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