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3 hours ago by

Hi, I'm a researcher using DESeq2 for hi-chip differential analysis.

When I performed differential analysis using DESeq2, I found that my data's MA plot is far non-symmetric.(Even for not significant values)

I thought it can happen because it's not RNA-seq data. But I can't explain exactly why.

non symmetric MA plot example for my hi-chip data
I have three questions here.

  1. Does someone know what's the meaning of non-symmetric MA plot in DESeq2 for the data? Can this happen or should I think my data is not good?
  2. If non-symmetric MA plot like this is not good, can I make it symmetric???
  3. Can I use DESeq2 for differential loop analysis??(My data's coverage is similar between samples)

Thank you for your help.

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