I've searched through the manual and bioconductor support, there doesn't seem to be a way to specify a custom normalization factor in DiffBind when analyzing using DESeq2. I'm wondering if there is a relatively easy "hacky" way to do this? Thanks in advance for your help.

I'm expecting to add a straightforward way to supply normalization factors explicitly before the next release.

In the meantime, there is a hacky way to do this. When you are using the defaults method=DBA_DESEQ2 and bFullLibrarySize=TRUE, the normalization factors are set as follows:

libsize <- as.numeric(DBA$class['Reads',])
sizeFactors <- libsize/min(libsize)

You can change the values of DBA$class['Reads',] to whatever you like so that the final sizeFactors end up how you want them.

The latest version of DiffBind has a new interface function, dba.normalize(), that allows vectors of normalization factors and library sizes (or a matrix of normalization offsets) to be specified instead of using the internal normalization calculations.