Reporter genes, or rather the proteins they produce, can be analyzed directly by studying spectrophotometric properties or enzymatic activity, or indirectly through antibody-based assays.

Generally, enzymatic assays are more sensitive because they require only a small amount of reporter enzyme to produce detectable reaction products. However, a potential drawback is the high background if the cell has endogenous enzymatic activity such as β-galactosidase breaking down lactose. 

Antibody-based assays are typically less sensitive but their advantage is the ability to detect the reporter protein regardless of its enzymatic activity. Essentially, a reporter assay uses a protein to measure a biological outcome through an observable parameter such as bioluminescence.