Non-symmetric MA-plot (DESeq2)
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2.5 years ago
mdidish • 0

Hello,

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: genotype effect
  • diet effect: diet effect
  • interaction genotype and diet: interaction

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?

Best.

MA-plot DESeq2 • 462 views
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