Deseq plots interpretation · Biostar

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Deseq plots interpretation

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:

https://ibb.co/joeJtx

rna-seq

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updated 8.5 years ago by Kevin Blighe

• written 8.5 years ago by phur •

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

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written 8.5 years ago by kautilya

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.

Thanks.

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written 8.5 years ago by Kevin Blighe

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