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Qualitative assessment of cDNA microarray gene expression data using detrended fluctuation analysis

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  • Nagarajan, Radhakrishnan
  • Upreti, Meenakshi
  • Govindan, R.B.

Abstract

A number of microarray studies assume gene expression data to be independent of one another. In this report, we provide evidence of correlation in cDNA microarray gene expression data using classical power spectral analysis and the sophisticated detrended fluctuation analysis (DFA). Such correlations are shown to be an outcome of gene's position on the arrays and immune to pre-processing procedures such as normalization. The results presented encourage DFA as a tool for qualitative assessment of microarray gene expression data prior to inferring differential gene expression.

Suggested Citation

  • Nagarajan, Radhakrishnan & Upreti, Meenakshi & Govindan, R.B., 2007. "Qualitative assessment of cDNA microarray gene expression data using detrended fluctuation analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 373(C), pages 503-510.
    • Handle: RePEc:eee:phsmap:v:373:y:2007:i:c:p:503-510
    DOI: 10.1016/j.physa.2006.04.064
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    References listed on IDEAS

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    1. Li, S.P. & Tseng, J.J. & Wang, S.C., 2005. "Reconstructing gene regulatory networks from time-series microarray data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 350(1), pages 63-69.
    2. Blasi, Monica Francesca & Casorelli, Ida & Colosimo, Alfredo & Blasi, Francesco Simone & Bignami, Margherita & Giuliani, Alessandro, 2005. "A recursive network approach can identify constitutive regulatory circuits in gene expression data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 348(C), pages 349-370.
    3. Farkas, I. & Jeong, H. & Vicsek, T. & Barabási, A.-L. & Oltvai, Z.N., 2003. "The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 318(3), pages 601-612.
    4. Kantelhardt, Jan W & Koscielny-Bunde, Eva & Rego, Henio H.A & Havlin, Shlomo & Bunde, Armin, 2001. "Detecting long-range correlations with detrended fluctuation analysis," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 295(3), pages 441-454.
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    Cited by:

    1. Zheng, Hongyang & Song, Weiguo & Wang, Jian, 2008. "Detrended fluctuation analysis of forest fires and related weather parameters," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 387(8), pages 2091-2099.

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