Question: MA plot scattering pattern
0
gravatar for avitalwasser
5 months 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 • 141 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by avitalwasser0

it was very helpful, thanks !

ADD REPLYlink written 5 months ago by avitalwasser0
Answer: MA plot scattering pattern
0
gravatar for Michael Love
5 months ago by
Michael Love23k
United States
Michael Love23k 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 5 months ago by Michael Love23k
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