Is it somehow possible to do a chipseq experiment with two factors (treatment, no treatment), (antibody of interest, control Ig antibody)? I believe that one could do this with edgeR utilizing count data from chipseq and creating a DGEList with the group representing each individual chipseq run, and then creating a design matrix to calculate norm factors, estimate dispersion, and perform glmQLFtests (following p.8 of the edgeR manual)?
What do you mean by each individual ChIP-seq run? The ChIP sample and its negative control? If so, the answer is technically yes. You can use the "run" as the blocking factor and have another set of terms for the treatment-specific log-fold change of the ChIP over the control. This can be fed through the GLM machinery in edgeR, e.g., to compare the log-fold changes between treatment conditions to identify DB regions.
In practice, this may not do what you expect. The argument for using the log-fold change in the differential comparisons is that chromatin states change across conditions, altering accessibility and thus background coverage. The aim is to compute a condition-specific log-fold change to "cancel out" the change in background coverage that isn't that interesting to us. Unfortunately, changes in chromatin state are often correlated with actual changes in binding, i.e., you get more protein binding at a location because the chromatin opens up. This means that any adjustment for chromatin state would also cancel out some or all of the changes in binding.
For example, let's say that my DNA was twice as open in my treatment condition compared to non-treatment at a particular genomic site. As a result of the increased accessibility, I also have twice as much binding of my protein of interest at this site. The two effects would cancel out when I computed my log-fold change for this condition, rendering me unable to detect differential binding between conditions. This is an inevitable result of "subtracting" the input effect in a log-link model, see A: csaw with negative controls for more details.