Question

X-axis of MAplot and lfcShrink

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Yuya Liang ▴ 20

@yuya-liang-14202

Last seen 5.7 years ago

United States

Hi everyone,

The X-axis of my plot looks strange. Why the mean of normalized counts is super small? (My X-axis is 1e+01, 1e+05 but demo plot is 1, 100, 10000)

Due to the shape of MA plot, I suppose to shrunk the log2 fold changes. I used lfcShrink() to do it but the result doesn't look like a output from results().

Thank you!

deseq2 • 1.3k views

ADD COMMENT • link 6.5 years ago • updated 6.2 years ago Yuya Liang ▴ 20

score 1 · Answer 1 · 2017-10-20

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Michael Love 41k

@mikelove

Last seen 8 hours ago

United States

These numbers aren't super small, they represent powers of 10. 1e3 = 1,000, 1e5=100,000

ADD COMMENT • link 6.5 years ago Michael Love 41k

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Thank you, Sir! I didn't notice it's 1e+05 instead of 1e-05. Do you happen to know lfcShrink( ) problem?

ADD REPLY • link 6.5 years ago Yuya Liang ▴ 20

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The command you used will work fine with the next version of DESeq2 (released this month). But for your version, you need to include res=res. This is also explained in the help page for the function. This is always the first place you should look if you have a question about a function:

You type into R:

?lfcShrink

And hit <return> and then look at the arguments, and the returned value, in particular.