The article is terrible as usual from Alpha and similar to all the fluff / pump / dump pieces from Fool these days. They literally tell you bland, incorrect facts (see my reply at the bottom of the article on Alpha) and give you meaningless opinion for both sides - hard to be wrong when they do that. Their intent is solely to lure you into buying their premium reports. Mr. Daly author of the Alpha article is a retired insurance guy with weekend investment experience. The Fool article from yesterday has similar intent and pedigree.
That said, I agree with you that Affy has a huge upside - consensus rev. estimate for 2013 is $161M with compounding 100% y/y growth projected for next two years at minimum. That puts the stock versus similar growth bios at beginning of 2014 at $40 - $60/share conservatively.
Unless Omontys actually performs poorly, which seems very unlikely now based on the word on the street/clinics from the 10K users at Fres., this is as good as an investment opportunity that you will find these days. Usually, investors are waiting for approval, product roll-out, adoption, etc. In this case we have a proven, gigantic market (even if smaller than in the past), a two-horse raise against an aging pricey incumbent that customers hate (I've talked to the MDOs), and already they have great initial market adoption with the largest operator (Fres) and five of six of the MDOs. It just doesn't line up any better than that.
So, weather the stock fluctuation during this initial couple of quarters after launch. You will be hard-pressed to find another 100% yearly growth opportunity that doesn't rely on one-time events.