A fluidics station is not cheap, and neither is the rest of the typical Affy rig (and Illumina is worse), but having set up more than a few, I have to tell you,

A fluidics station is not cheap, and neither is the rest of the typical Affy rig (and Illumina is worse), but having set up more than a few, I have to tell you, the cost of the components isn't actually very great. (As in, the parts and labor. The price paid to the company is most assuredly huge.) If there were actually demand for it, someone could throw together the equivalent of an open-source array reader kit for (guesing, but not without basis in fact) $10K or so. God knows it's faster and easier to work around Affy or Illumina's junkware with R than it is to get anything done with their binaries... but that would be silly because who outside of a hospital or lab really has that much use for one? But sequencing-by-synthesis methods that can use WGA on small samples are the key to a truly accessible and useful map of an individual's genome. I don't really care how my genome differs from Craig Venter's; I want to know how it differs from itself as I get older, I want to know how it differs from itself as I am exposed to environmental factors, and I want to know how it differs from the baseline for my 'eigen-ancestry' in terms of disease risk. There are so many statistical piles of shit that have already been stepped in (particularly WRT linkage analysis, but I'm sure we'll eventually see a good laffer from a GWAS of some sort now that they're all the rage) that I'd really rather have the tools to work on my own, thankyouverymuch...