Affymetrix, Inc. (AFFX)

I am a professor at a research institute and do work in the biomedical field. I wouldn't touch Affy stock with a ten foot pole for three major reasons:
1) Their product is inferior to the Illumina chip. They got a very bad reputation when they released their 500K chip last year because over 1 out of 4 (!!) of the SNPs in there were garbage. Most researchers I know who were burned by that experience are going Illumina from here on out. Illumina has a much better reputation.

2) Much of their revenue comes indirectly from the government, via research grant funding in academia. Research funding under the Bush presidency has gotten bad, and given the debt this administration has accumulated, I can't see how this can change quickly, even with a Democrat in office. Granted, Affy makes money from private industry too, but one chunk of the income they could potentially tap into is dwindling.

3) Affy's main business is in making SNP chips (single nucleotide polymorhpism chps). However, SNPs are already becoming passe. Overall, the promise of SNP chips (and association studies) were way overblown. The reality is turning out to be much much more humble than we were promised ten years ago. The new thing (and this one probably will work) is in sequencing every single base pair in the genome. I won't get technical, but this really is the end game in genetics. How is Affy positioned for this new technology?