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Question: The descriptions of score methods in DiffBind
0
gravatar for Gary
11 months ago by
Gary0
Gary0 wrote:

Hi,

The descriptions of score methods in DiffBind manual are trimmed and cannot be understood in its pdf file (fig1). Could you provide them for me to learn? Many thanks. By the way, the default is DBA_SCORE_TMM_MINUS_FULL?

Best,

Gary

fig1

fig1

ADD COMMENTlink modified 11 months ago by Rory Stark2.1k • written 11 months ago by Gary0
1
gravatar for Rory Stark
11 months ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

You are correct about the default score, however this is only used for plots, and only when the entire experiment if plotted. When data form a speicic contrast is used, the normalised counts from that comparison are plotted and/or reported.

The best way to get all the text is within R:

> library(DiffBind)
> ?dba.count

Cheers-

Rory

ADD COMMENTlink written 11 months ago by Rory Stark2.1k

Thank you so much for your help.

ADD REPLYlink written 11 months ago by Gary0
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