preprocess.poobah

preprocess.poobah(sig)

Detection p-values against the out-of-band background (Zhou 2018).

For each probe, the probability that a signal at least this bright would be seen from background alone, read off the empirical distribution of the out-of-band intensities in the relevant channel. A type I probe is compared against its own channel’s null in both beads; a type II probe’s methylated bead is green and its unmethylated bead is red, so it is compared against both nulls.

The p-value is the smaller of the two tail probabilities, i.e. the more optimistic bead. A probe is detected if either of its beads rose above background, which is the right question: a fully methylated probe has almost no unmethylated signal by construction, and requiring both would fail every probe at an extreme.