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Question: MA plot scattering pattern
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gravatar for avitalwasser
16 days ago by
avitalwasser0 wrote:

Hi,

I'm new at bioinformatics and use DESeq2 for the first time. I'm analyzing a RNA-seq data - 3 WT replicate and 3 mutant replicates. The MA plot show diagonal lines and I'm not sure if it's normal, or what it means. It looks too nit to me.

any ideas?

picture in the link

https://www.scribd.com/document/394171998/MAplot-DESeq2-Res

thanks in advance !

ADD COMMENTlink modified 14 days ago • written 16 days ago by avitalwasser0

it was very helpful, thanks !

ADD REPLYlink written 14 days ago by avitalwasser0
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gravatar for Michael Love
16 days ago by
Michael Love20k
United States
Michael Love20k wrote:

Those lines represent ratios of integers, e.g. 2/1, 3/1, 3/2, etc.

You can shrink these lines using lfcShrink() which provides reliable posterior estimates of LFC. See vignette.

ADD COMMENTlink written 16 days ago by Michael Love20k
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