Output of normalizing a dba object with DBA_DESEQ2,normalize = DBA_NORM_RLE in Diffbind
1
0
Entering edit mode
Alexandre • 0
@095e334e
Last seen 2 days ago
Hong Kong

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

DiffBind • 98 views
ADD COMMENT
1
Entering edit mode
Rory Stark ★ 4.0k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

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.

ADD COMMENT
0
Entering edit mode

thanks a lot @Rory , that clarifies things to me.

ADD REPLY

Login before adding your answer.

Traffic: 455 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6