Diffbind multiple blocking factor
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bioinfouser2 ▴ 10
@bioinfouser2-15147
Last seen 11 months ago
1. In Diffbind package, I want to block multiple factors, e.g. Tissue, condition and factor. In the Vignette, there's example for blocking only one category, not all 2 or 3 together. How can it be done? Thank you very much in advance!

2. Also, I tried to block using multiple factor like this:



"block=c(DBA_CONDITION,DBA_TISSUE, DBA_FACTOR)"

Is it the correct way?

1. I am seeing this warning when I tried the 2nd way of blocking:
Warning messages:
A blocking value applies to all samples in both groups


Can someone please explain what to do for this warning? As a matter of fact, after this, blocking doesn't work, when the warning shows up.

diffbind rory stark chip seq • 270 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 14 hours ago
CRUK, Cambridge, UK

Blocking in DiffBind is used to identify matched samples across groups. For example, batches or tumor-normal pairs. The warning is that you are specifying a blocking factor that has the same value for all of the samples, so there is no way to treat them differently.

Think in terms of the two groups of samples that form the two sides of the contract, and provide a factor that has different values for different samples, but where each block value applies to at least one sample in each group.

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Dear Rory, Thank you for your reply! I understand now. However, I am wondering, is it similar to the linear modelling concept applied in to DESeq2/EdgeR or other kinds of tools?

Also, if you could kindly let me know whether DiffBind can take multiple blocking factor or not. As I have almost 4-5 blocking factors, I am still not sure whether DIffBind can have multiple blocking factors. I couldn't find documentation regarding it.

Thanks a lot for taking your time help us!

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Dear Rory, Thank you for your reply! I understand now. However, I am wondering, is it similar to the linear modelling concept applied in to DESeq2/EdgeR or other kinds of tools?

Also, if you could kindly let me know whether DiffBind can take multiple blocking factor or not. As I have almost 4-5 blocking factors, I am still not sure whether DIffBind can have multiple blocking factors. I couldn't find documentation regarding it.

Thanks a lot for taking your time help us!

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Internally, it is using a GLM that is basically

 ~block + group

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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 14 hours ago
CRUK, Cambridge, UK

The upcoming release of DiffBind will support the ability to include arbitrary designs and complex contrasts, made up of any of the metadata factors Tissue, Factor, Condition, Treatment, Replicate, and Caller. So one could for example have a design such as:

~Replicate + Treatment + Condition + Tissue
`

and set any of the design matrix coefficients however you like for testing (e.g. Tissue1 - Tissue2).

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That is superb! Cannot wait to use the updated version!

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If you're interested in trying if before the release in a few months, it should be available within 24 hours to download and install here: https://bioconductor.org/packages/3.12/bioc/html/DiffBind.htm

Any version after 2.99.1 has the ability to handle arbitrary design formulae. I am available to help as I am interested in having it tested by some users before release.

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This functionality has now been released in the current version.