I have a dba object which I do not provide as input bamControl bam control files, i.e. my design.csv file does not have the bamControl column.

eprint <- dba(sampleSheet = "design.csv",config=data.frame(doBlacklist=FALSE, doGreylist=FALSE))

I then normalize eprint in the following manner:

eprint <- dba.normalize(eprint,method = DBA_DESEQ2,normalize = DBA_NORM_RLE,bRetrieve = T)
eprint

> eprint
$norm.method
[1] "RLE"

$norm.factors
   ep_293T_siNeg_R1    ep_293T_siNeg_R2    ep_293T_siFUS_R1 
          0.9845496           1.2404820           1.4671065 
   ep_293T_siFUS_R2 input_293T_siNeg_R1 input_293T_siNeg_R2 
          1.8836897           0.6629589           1.0861656 
input_293T_siFUS_R1 input_293T_siFUS_R2 
          0.8100974           0.8094561 

$lib.method
[1] "RiP"

$lib.sizes
   ep_293T_siNeg_R1    ep_293T_siNeg_R2    ep_293T_siFUS_R1 
            7557248            10526927            10930156 
   ep_293T_siFUS_R2 input_293T_siNeg_R1 input_293T_siNeg_R2 
           15823958             6687127            10837242 
input_293T_siFUS_R1 input_293T_siFUS_R2 
            7727720             8181321 

$control.subtract
[1] TRUE

$filter.value
[1] 1

I would then expect that $control.subtract=FALSE since control$subtract means if control reads were subtracted from the read counts.

What am I missing here ? Thanks

Functionally, this is doing exactly what you want: as there are no control files, "subtracting" them has no effect.

If no greylists are applied, the default is to set $control.subtract to TRUE. I can see how it may be more clear in future for DiffBind to recognize that nothing is actually being subtracted and to set the $control.subtract field to FALSE.