Statistical calibration of qRT-PCR, microarray and RNA-Seq gene expression data with measurement error models

DOI10.1214/14-AOAS721MaRDI QIDQ400646zbMATH OpenFDO

Authors Zhaonan Sun, Thomas Kuczek, Yu Zhu

Publication date 22 August 2014

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1212.6690

zbMATH Keywords

comparative calibrationfunctional and structural parametersgene differential expressiontranscriptone profiling

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10)

Abstract: The accurate quantification of gene expression levels is crucial for transcriptome study. Microarray platforms are commonly used for simultaneously interrogating thousands of genes in the past decade, and recently RNA-Seq has emerged as a promising alternative. The gene expression measurements obtained by microarray and RNA-Seq are, however, subject to various measurement errors. A third platform called qRT-PCR is acknowledged to provide more accurate quantification of gene expression levels than microarray and RNA-Seq, but it has limited throughput capacity. In this article, we propose to use a system of functional measurement error models to model gene expression measurements and calibrate the microarray and RNA-Seq platforms with qRT-PCR. Based on the system, a two-step approach was developed to estimate the biases and error variance components of the three platforms and calculate calibrated estimates of gene expression levels. The estimated biases and variance components shed light on the relative strengths and weaknesses of the three platforms and the calibrated estimates provide a more accurate and consistent quantification of gene expression levels. Theoretical and simulation studies were conducted to establish the properties of those estimates. The system was applied to analyze two gene expression data sets from the Microarray Quality Control (MAQC) and Sequencing Quality Control (SEQC) projects.

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Cited in

(3)

• A nonlinear mixed-effects model for estimating calibration intervals for unknown concentrations in two-color microarray data with spike-ins
• Statistical calibration of qRT-PCR, microarray and RNA-Seq gene expression data with measurement error models
• Calibration of quantitative PCR assays

Describes a project that uses

Uses Software

• DEseq
• GPSeq

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