Question: Deseq plots interpretation
gravatar for sally009
22 months ago by
sally0090 wrote:

Hi, I am new to RNA-Seq and I have analyzed RNA-Seq datasets containing five normal replicates and three treated replicates. I have done the deseq2 and got some plots but I am not able to see the pattern in the data or interpret the data. Can anybody please suggest me on how I could approach this problem? I read the manuals and about the plots but I am not getting it.

MA plot:

rna-seq • 611 views
ADD COMMENTlink modified 22 months ago by Kevin Blighe52k • written 22 months ago by sally0090

Can you be more specific about any particular aspects/plots that you are not understanding?

ADD REPLYlink written 22 months ago by kautilya400

I edited the post so that you can access the figure, a MA plot. It does not look typical. Can you share the following with us:

  • Which data are you analysing?
  • How did you align the data?
  • How did you derive raw counts?
  • Did you input raw or normalised counts into DESeq2?

Finally, paste your DESeq2 commands here.


ADD REPLYlink modified 22 months ago • written 22 months ago by Kevin Blighe52k
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