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

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• 作者：Yunfeng Yang (1)
  Mengxia Zhu (2)
  Liyou Wu (1) (3)
  Jizhong Zhou (1) (3)
  
• 刊名：BMC Genomics
• 出版年：2008
• 出版时间：September 2008
• 年：2008
• 卷：9
• 期：2-supp
• 全文大小：1165KB
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• 作者单位：Yunfeng Yang (1)
  Mengxia Zhu (2)
  Liyou Wu (1) (3)
  Jizhong Zhou (1) (3)
  
  1. Biosciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
  2. Computer Science Department, Southern Illinois University, 62901, Carbondale, IL, USA
  3. Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, 73019, Norman, OK, USA
  

文摘

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.