There are known sources of variability in analysis results, including pool imbalance (if an assay has more than one pool of amplicons), total number of reads, per-amplicon attributes of GC proportion, and length of the amplicon insert. In practice, other variability exists that is not associated with known attributes, yet is systematic. Copy number baselines, when added to a workflow can correct the variability.
Analysis workflows that use baseline controls allow you to determine copy number changes in the sample of interest, without the use of a matched control.
In Ion Reporter™ Software, copy number baseline workflow presets are the components that you can add to analysis workflows as baseline controls.
