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.

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.

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).