Question: DESeq2 MA plot look different
0
gravatar for jshouse
22 months ago by
jshouse0
jshouse0 wrote:

In the past, (DESeq2 versions < 1.1.4), MA plots from DESeq2 looked like the following (formatting modified by me, but you get the idea).

OLD MA plot

MA plots since 1.14 look different. Is there any reason to be alarmed at how the distribution of l2fc's is dramatically different in its randomness at low count thresholds?

new plot

 

 

deseq2 maplot • 584 views
ADD COMMENTlink modified 22 months ago by Michael Love24k • written 22 months ago by jshouse0
Answer: DESeq2 MA plot look different
0
gravatar for Michael Love
22 months ago by
Michael Love24k
United States
Michael Love24k wrote:

See here:

New function lfcShrink() in DESeq2

We updated the vignette code and workflow code as well, and such changes can always be found in NEWS

ADD COMMENTlink written 22 months ago by Michael Love24k

Thanks Michael,

I didn't catch that. Sorry for wasting your time. I will look there first next time.

 

ADD REPLYlink written 22 months ago by jshouse0

No problem. It’s still a new function. We’re developing new features based on this, to be released in October.

ADD REPLYlink written 22 months ago by Michael Love24k
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