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Question: MA plot scattering pattern
0
gravatar for avitalwasser
12 weeks 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 !

deseq2 maplot • 106 views
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by avitalwasser0

it was very helpful, thanks !

ADD REPLYlink written 12 weeks ago by avitalwasser0
Answer: MA plot scattering pattern
0
gravatar for Michael Love
12 weeks ago by
Michael Love22k
United States
Michael Love22k 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 12 weeks ago by Michael Love22k
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