I am trying to compare different controls for various ChIP-seq datasets. Accordingly, I have experiments with the same BAM experiment file (bamReads), but with different control BAM files (bamControl). Therefore, I have multiple sample lines with the same bamReads, but different bamControl values.

I receive the following error, upon invoking ChIPQC upon my samples:

Error in ChIPQC(samples, summits = 250, annotation = "mm9", chromosomes = chromosomes,  :
  Unable to process. Each bam file must be associated with at most one peakset.

How can I get ChIPQC to function in this context?