Preprocessing forms an oft-neglected foundation for a wide range of statistical and scientific analyses. However, it is rife with subtleties and pitfalls. Decisions made in preprocessing constrain all later analyses and are typically irreversible. Hence, data analysis becomes a collaborative endeavor by all parties involved in data collection, preprocessing and curation, and downstream inference. Even if each party has done its best given the information and resources available to them, the final result may still fall short of the best possible in the traditional single-phase inference framework. This is particularly relevant as we enter the era of "big data". The technologies driving this data explosion are subject to complex new forms of measurement error. Simultaneously, we are accumulating increasingly massive databases of scientific analyses. As a result, preprocessing has become more vital (and potentially more dangerous) than ever before.