Batch effects are everywhere! Deflategate edition

Rafael Irizarry

In my opinion, batch effects are the biggest challenge faced by genomics research, especially in precision medicine. As we point out in this review, they are everywhere among high-throughput experiments. But batch effects are not specific to genomics technology. In fact, in this 1972 paper (paywalled), WJ Youden describes batch effects in the context of measurements made by physicists. Check out this plot of astronomical unit speed of light estimates with an estimate of spread confidence intervals (red and green are same lab).

Sometimes you find batch effects where you least expect them. For example, in the deflategate debate. Here is quote from the New England patriot’s deflategate rebuttal (written with help from Nobel Prize winner Roderick MacKinnon) in other words, the Colts balls were measured after the Patriots balls and had warmed up more. For the above reasons, the Wells Report conclusion that physical law cannot explain the pressures is incorrect.

Here is another one:

In the pressure measurements physical conditions were not very well-defined and major uncertainties, such as which gauge was used in pre-game measurements, affect conclusions.

So NFL, please read our paper before you accuse a player of cheating.

Disclaimer: I live in New England but I am Ravens fan.