Methodology article

Estimating accuracy of RNA-Seq and microarrays with proteomics

Xing Fu^1* , Ning Fu^1* , Song Guo² , Zheng Yan² , Ying Xu² , Hao Hu^2,3 , Corinna Menzel³ , Wei Chen³ , Yixue Li¹ , Rong Zeng¹ and Philipp Khaitovich^2,4

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

author email corresponding author email* Contributed equally

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

Published:	16 April 2009

Abstract

Background

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.

Results

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.

Conclusion

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.