Question: Diffbind GLM Design
gravatar for liruiradiant
5 weeks ago by
United States
liruiradiant0 wrote:

Hello Rory,

Thanks for the Diffbind package, it makes DB analysis very easy.

However, I have the following question: How does DiffBind handle Input samples and how does it compare condition B with condition A? For example, I have a experiment design like this:

Condition    A    B
IP           2     2
IN           2     2

The number 2 indicates 2 biological replicates for each cell.

When DiffBind calls DESeq2, what contrast does it use internally to calculate LFC and FDR between condition A and B?

1. A_IP  - B_IP
2. (A_IP - A_IN) - (B_IP - B_IN) 
3. sth. else?

Thank you!


diffbind • 50 views
ADD COMMENTlink modified 24 days ago by Rory Stark3.0k • written 5 weeks ago by liruiradiant0

I think when Input was not specified in the meta data, then '1' is used. When Input is provided, '2' is used?

ADD REPLYlink written 24 days ago by liruiradiant0
Answer: Diffbind GLM Design
gravatar for Rory Stark
24 days ago by
Rory Stark3.0k
CRUK, Cambridge, UK
Rory Stark3.0k wrote:

The Input reads are not used in the DESeq2 modelling itself. By default, these reads are subtracted from the ChIP reads prior to modelling, you can control this using the bSubControl parameter when calling dba.analyze().

ADD COMMENTlink written 24 days ago by Rory Stark3.0k
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