Prior to its widespread use in the past three decades radioactivity was the most common label.
The advantages of fluorescence over radioactive labels are as follows:
* Fluorescence is safer to use and does not require radiological controls.
* Several fluorescent molecules can be used simultaneously given that they do not overlap, cf. FRET, whereas with radioactivity two isotopes can be used (tritium and a low energy isotope such as P due to different intensities) but require special machinery (a tritium screen and a regular phosphor-imaging screen or a specific dual channel detector).
Note: a channel is similar to "colour" but distinct, it is the pair of excitation and emission filters specific for a dye, e.g. agilent microarrays are dual channel, working on cy3 and cy5, these are colloquially referred to as green and red.
Fluorescence is not necessarily more convenient to use because it requires specialized detection equipment of its own. For non-quantitative or relative quantification applications it can be useful but it is poorly suited for making absolute measurement because of fluorescence quenching, whereas measuring radioactively labeled molecules is always direct and highly sensitive.
Disadvantages of fluorophores include:
* Significantly changes the properties of a fluorescently-labeled molecule
* Interference with normal biological processes
* Toxicity