Question

toptable sort .by set

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snowmattin • 0

@69358726

Last seen 23 months ago

Germany

Dear guys,

I am trying to use limma to find the DEGs, and the topTable function has a parameter sort.by, which explains that "p" for "P", so when code as topTreat(fit, coef=1, sort.by="p", resort.by=NULL, ...) , is it sort by p-value or adjusted p-value?

Thanks a lot!

https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/toptable

limma rnaseqGene • 1.1k views

ADD COMMENT • link 2.5 years ago snowmattin • 0

score 1 · Answer 1 · 2022-05-13

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Gordon Smyth 51k

@gordon-smyth

Last seen 5 hours ago

WEHI, Melbourne, Australia

Sorting by p-value is the same as sorting by adjusted p-value.

ADD COMMENT • link 2.5 years ago Gordon Smyth 51k

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Thanks a lot! What if the p-value has much difference from the adjusted p-value?

ADD REPLY • link 2.5 years ago snowmattin • 0