Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays

TL;DR

This paper introduces a more accurate gamma-normal model for background correction in Illumina BeadArrays, improving fit and bias but not sensitivity, challenging previous exponential-based assumptions.

Contribution

It proposes a gamma-normal distribution model for signal and noise, providing a better fit for Illumina BeadArray data compared to the traditional normal-exponential model.

Findings

The gamma-normal model fits observed intensities more accurately.

Background correction based on the gamma-normal model reduces bias.

Sensitivity does not improve despite better modeling accuracy.

Abstract

Motivation: Illumina BeadArray technology includes negative control features that allow a precise estimation of the background noise. As an alternative to the background subtraction proposed in BeadStudio which leads to an important loss of information by generating negative values, a background correction method modeling the observed intensities as the sum of the exponentially distributed signal and normally distributed noise has been developed. Nevertheless, Wang and Ye (2011) display a kernel-based estimator of the signal distribution on Illumina BeadArrays and suggest that a gamma distribution would represent a better modeling of the signal density. Hence, the normal-exponential modeling may not be appropriate for Illumina data and background corrections derived from this model may lead to wrong estimation. Results: We propose a more flexible modeling based on a gamma distributed signal and a normal distributed background noise and develop the associated background correction. Our model proves to be markedly more accurate to model Illumina BeadArrays: on the one hand, this model offers a more correct fit of the observed intensities. On the other hand, the comparison of the operating characteristics of several background correction procedures on spike-in and on normal-gamma simulated data shows high similarities, reinforcing the validation of the normal-gamma modeling. The performance of the background corrections based on the normal-gamma and normal-exponential models are compared on two dilution data sets. Surprisingly, we observe that the implementation of a more accurate parametrisation in the model-based background correction does not increase the sensitivity. These results may be explained by the operating characteristics of the estimators: the normal-gamma background correction offers an improvement in terms of bias, but at the cost of a loss in precision.