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

Question

[bright602]

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!

Answer 1

[e.rempel]

Hi,

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

dba.object$config$th <- .01

Answer 2

[jared.andrews07]

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

Answer 3

[FatihSarigol]

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.