* Relatively low array size: Although it has the potential to use an increased amount of dyes to generate millions of different array elements, the current generation of commercially available microsphere arrays (from Luminex xMAP technology) only uses two sets of dyes and therefore can only detect ~100 targets per experiment.
* Hybridization between different sets of probes and target sequences requires a specific annealing temperature, which is affected by length and sequence of the oligonucleotide probe. Therefore, for every experiment, only one possible annealing temperature can be used. Thus, all probes used in given experiment must be designed to hybridize to the target at the same temperature. Although introducing base pair mismatch in some sets of the probes could minimize annealing temperature differences between each set of probes, the hybridization problem is still significant if more than 10-20 targets are tested in one reaction.