I read through the other posts about using RNA-seq packages to analyze Chip-seq data (https://support.bioconductor.org/p/72098/). It seems like the general consensus is to just ignore the input control samples or build a black-list and look at differential binding between IP samples.
If I do want to incorporate input control into my differential binding, is it valid to include that data as another factor in the design matrix and perform a difference of difference?
So for every library, I would have a "IP" factor with two levels (IP/Input) and also a "sample" factor with two levels for treatment and control.
I am not very well versed in R, would it be possible to make this kind of contrast? And would this type of contrast even be valid?