Limitations of microarrays

Although microarrays have great potential in genomics and comparative genomics research, they have a number of limitations too:

-They require a large amount of high-quality mRNA, which can be difficult to acquire.

-Varying protocols are required, depending on the goals and priorities of the experiment (whether high-throughput is necessary, low-abundance transcripts are important, what tissue types are to be used, etc.)‏

-They are still very expensive.

-Analyzing the results requires a high level of technical skill and software.

-Artifacts are common!