Comparison of the latest commercial short and long oligonucleotide microarray technologies. Academic Article uri icon

Overview

abstract

  • BACKGROUND: We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip, GE Healthcare CodeLink and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. RESULTS: All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms. CONCLUSION: We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels.

publication date

  • March 15, 2006

Research

keywords

  • Oligonucleotide Array Sequence Analysis

Identity

PubMed Central ID

  • PMC1473202

Scopus Document Identifier

  • 33744804832

Digital Object Identifier (DOI)

  • 10.1038/sj.leu.2403136

PubMed ID

  • 16539734

Additional Document Info

volume

  • 7