Question

How to change the default P value and FDR cutoff in DiffBind

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4.5 years ago

bright602 ▴ 50

Hi, I would like to know how to change the default P value and FDR cutoff in DiffBind if I use DBA_DESEQ2 for the differential analysis? Thanks a lot!

ChIP-Seq R • 2.5k views

ADD COMMENT • link updated 2.8 years ago by FatihSarigol ▴ 260 • written 4.5 years ago by bright602 ▴ 50

score 1 · Answer 1 · 2020-06-25

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4.5 years ago

e.rempel ★ 1.1k

Hi,

p-value cutoff is specified in the entry dba.object$config$th. You can directly change it

dba.object$config$th <- .01

ADD COMMENT • link 4.5 years ago by e.rempel ★ 1.1k

score 1 · Answer 2 · 2020-06-25

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4.5 years ago

jared.andrews07 ★ 18k

The th and fold parameters in the dba.report function are what you need to tweak.

ADD COMMENT • link 4.5 years ago by jared.andrews07 ★ 18k

score 0 · Answer 3 · 2022-02-28

By default the threshold is set with FDR, so changing the th value will change the FDR threshold. To use p-value instead, use this option after generating your object using dba

MyDbaObject$config$bUsePval <- TRUE

same way you can also change the p-value threshold next

MyDbaObject$config$th <- 0.01

then continue the analysis with normalizing and reading the counts etc.