DESeq2 MA plot look different
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jshouse ▴ 10
@jshouse-10956
Last seen 10 months ago

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 • 1.4k views
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@mikelove
Last seen 12 hours ago
United States

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

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Thanks Michael,

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

 

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

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