Selecting reliable mRNA expression measurements across platforms improves downstream analysis

Pan Tong, Lixia Diao, Li Shen, Lerong Li, John Victor Heymach, Luc Girard, John D. Minna, Kevin R. Coombes, Lauren Averett Byers, Jing Wang

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

With increasing use of publicly available gene expression data sets, the quality of the expression data is a critical issue for downstream analysis, gene signature development, and cross-validation of data sets. Thus, identifying reliable expression measurements by leveraging multiple mRNA expression platforms is an important analytical task. In this study, we propose a statistical framework for selecting reliable measurements between platforms by model-ing the correlations of mRNA expression levels using a beta-mixture model. The model-based selection provides an effective and objective way to separate good probes from probes with low quality, thereby improving the efficiency and accuracy of the analysis. The proposed method can be used to compare two microarray technologies or microarray and RNA sequencing measurements. We tested the approach in two matched profiling data sets, using microarray gene expression measurements from the same samples profiled on both Affymetrix and Illumina platforms. We also applied the algorithm to mRNA expression data to compare Affymetrix microarray data with RNA sequencing measurements. The algorithm successfully identified probes/genes with reliable measure-ments. Removing the unreliable measurements resulted in significant improvements for gene signature development and functional annotations.

Original languageEnglish (US)
Pages (from-to)81-89
Number of pages9
JournalCancer Informatics
Volume15
DOIs
StatePublished - 2016

Keywords

  • Beta-mixture model
  • Correlation coefficients
  • Cross-validation
  • Gene expression
  • Probe selection
  • RNA sequence

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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