Question

DESeq2 MA plot look different

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jshouse ▴ 10

@jshouse-10956

Last seen 15 months ago

United States

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 • 2.7k views

ADD COMMENT • link updated 6.5 years ago by Michael Love 41k • written 6.5 years ago by jshouse ▴ 10

score 0 · Answer 1 · 2017-10-05

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Michael Love 41k

@mikelove

Last seen 14 minutes 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

ADD COMMENT • link 6.5 years ago Michael Love 41k

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Thanks Michael,

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

ADD REPLY • link 6.5 years ago jshouse ▴ 10

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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.

ADD REPLY • link 6.5 years ago Michael Love 41k