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This article is part of the supplement: IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School

Open Access Research

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference

Yunfeng Yang1*, Mengxia Zhu2, Liyou Wu13 and Jizhong Zhou13

Author Affiliations

1 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA

2 Computer Science Department, Southern Illinois University, Carbondale, IL, USA, 62901, USA

3 Institute for Environmental Genomics, and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA

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BMC Genomics 2008, 9(Suppl 2):S5  doi:10.1186/1471-2164-9-S2-S5

Published: 16 September 2008

Abstract

Background

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality.

Results

Microarray experiments were performed in a γ-proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing Shewanella genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses.

Conclusion

These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.