Ok, so with the rush to ChIP-seq and all the hype (much of it deserved) around “next-generation” sequencing generally, you might think that arrays are dead as used for ChIP (i.e. ChIP-chip).
I don’t think this is going to happen for simple cost reasons. For the near future, there will be lots of genome-scale ChIP studies and, for these, I strongly support ChIP-seq. It is a lot cheaper for better data. But I see a strong trend toward ChIP studies targeted toward specific biological questions and often questions requiring large sample numbers (e.g. epigenetic changes is cancer).
The financial math really isn’t that hard; with ChIP-seq running ~$5000 for external users and ChIP-chip running at $660 for external users (NimbleGen single arrays), it seems pretty clear that if a fair number of samples are involved, ChIP-chip is the way to go. That is, unless high-res whole genome coverage is absolutely necessary (usually not).
Furthermore, for taking chances on experiments, $660/sample is a lot more appealing on a lab budget than $5000/sample, particularly when you consider that, in the real world, even poor testing of a speculative idea is going to take 2 or 3 samples at minimum (=~$15,000 for ChIP-seq vs $1980 for ChIP-chip). A lot of labs can blow $2000; blowing $15,000 really hurts.
Given this analysis, it seems to me that NimbleGen should really push the low end of the market – in other words, try to get the cost even lower on a per sample basis (for fewer spots). I think they are on the right track with their multiplex arrays, but development of these has been disappointingly slow, and last time I looked, the cost structure around the 4plex with 70K/quadrant really wasn’t very attractive.
I may revisit this topic another time, but that is it for now.