What does PLIER really do?

Abstract

Motivation: Our goal was to understand why the PLIER algorithm performs so well given its derivation is based on a biologically implausible assumption. Results: In spite of a non-intuitive assumption regarding the PM and MM errors made as part of the derivation for PLIER, the resulting probe level error function does capture the key characteristics of the ideal error function, assuming MM probes only measure non-specific binding and no signal.