The Good
Once optimized, the QX600 system is capable of intensive multiplexing that no other digital PCR machine on the market can match. Some of our assays can asses the copy number of over 6 different genes per well.
The Bad
Getting the hang of generating perfect droplets is time-intensive. Once you have your own handling optimized, the droplet generator machine itself is also quite prone to suddenly not working. I think this year we have had to have parts replaced in the generator 3 different times.
The Bottom Line
This system has great sensitivity and intense multiplexing capabilities, but it is hard to optimize. Even once you finally have everything ironed out, the droplet generator machine itself is sort of unreliable, breaking multiple times per year (with admittedly very high volume usage though).