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Open Access Highly Accessed Methodology article

Estimating accuracy of RNA-Seq and microarrays with proteomics

Xing Fu1, Ning Fu1, Song Guo2, Zheng Yan2, Ying Xu2, Hao Hu23, Corinna Menzel3, Wei Chen3*, Yixue Li1, Rong Zeng1 and Philipp Khaitovich24*

Author Affiliations

1 Key lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China

2 Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, PR China

3 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany

4 Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

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BMC Genomics 2009, 10:161  doi:10.1186/1471-2164-10-161

Published: 16 April 2009



Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute expression level accurately. At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown.


In this study, we evaluate relative accuracy of microarrays and transcriptome sequencing (RNA-Seq) using third methodology: proteomics. We find that RNA-Seq provides a better estimate of absolute expression levels.


Our result shows that in terms of overall technical performance, RNA-Seq is the technique of choice for studies that require accurate estimation of absolute transcript levels.