Russian version English version
Volume 7   Issue 2   Year 2012
Riabenko E.A.

Setting Up the Nonlinear Model of Experimental Data From DNA Microarrays

Mathematical Biology & Bioinformatics. 2012;7(2):554-566.

doi: 10.17537/2012.7.554.

References

  1. Hubbell E, Liu W-M, Mei R. Robust estimators for expression analysis. Bioinformatics. 2002;18(12):1585-1592. doi: 10.1093/bioinformatics/18.12.1585
  2. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biology. 2001;2(8):RESEARCH0032.
  3. Koltai H, Weingarten-Baror C. Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction. Nucleic acids research. 2008;36(7):2395-405. doi: 10.1093/nar/gkn087
  4. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249-264. doi: 10.1093/biostatistics/4.2.249
  5. Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association. 2004;99(468):909-917. doi: 10.1198/016214504000000683
  6. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proceedings of the National Academy of Sciences of the United States of America. 2001;98(1):31-36. doi: 10.1073/pnas.98.1.31
  7. Affymetrix. Guide to Probe Logarithmic Intensity Error (PLIER) Estimation. Technical note. http://media.affymetrix.com/support/technical/technotes/plier_technote.pdf (accessed 02 September 2012).
  8. Katz S, Irizarry RA, Lin X, Tripputi M, Porter MW. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC bioinformatics. 2006;7:464. doi: 10.1186/1471-2105-7-464
  9. McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics. 2010;11(2):242-253. doi: 10.1093/biostatistics/kxp059
  10. McCall MN, Irizarry RA. Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinformatics. 2011;12(1):369. doi: 10.1186/1471-2105-12-369
  11. The National Center for Biotechnology Information. Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/ (accessed 02 September 2012).
  12. Halperin A, Buhot A, Zhulina EB. Sensitivity, specificity, and the hybridization isotherms of DNA chips. Biophysical Journal. 2004;86:718-730. doi: 10.1016/S0006-3495(04)74150-8
  13. Abdueva D, Skvortsov D, Tavaré S. Non-linear analysis of GeneChip arrays. Nucleic acids research. 2006;34(15):e105. doi: 10.1093/nar/gkl435
  14. Heim T, Wolterink JK, Carlon E, Barkema GT. Effective affinities in microarray data. Journal of Physics: Condensed Matter. 2006;18:S525. doi: 10.1088/0953-8984/18/18/S03
  15. Held GA, Grinstein G, Tu Y. Relationship between gene expression and observed intensities in DNA microarrays – a modeling study. Nucleic acids research. 2006;34(9):e70. doi: 10.1093/nar/gkl122
  16. Binder H, Preibisch S, Berger H. Calibration of microarray gene-expression data. Methods in Molecular Biology. 2010;576(16):375-407.
  17. Krainer S. Microarray based real-time analysis of nucleic acid hybridization kinetics and thermodynamics. Dissertation, Dept. of Biology, Johannes Gutenberg-Universitat Mainz, 2011.
  18. Davis S, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics. 2007;14:1846-1847.
  19. Huber W, Irizarry RA, Gentleman R. In: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Eds. Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S. New York: Springer Science+Business Media, 2005. P. 3-12.
  20. Affymetrix. Sample Data, Gene 1.0 ST Data Set. http://www.affymetrix.com/support/technical/sample_data/gene_1_0_array_data.affx (accessed 02 September 2012).
  21. Cichocki A, Cruces S, Amari S. Generalized Alpha-Beta Divergences and Their Application to Robust Nonnegative Matrix Factorization. Entropy. 2011;13(1):134-170. doi: 10.3390/e13010134
  22. Press WH, Teukolsky SA, Vetterling WT, Flannery BP. Numerical Recipes: The Art of Scientific Computing (3rd ed.). New York: Cambridge University Press, 2007. 1256 p.
Table of Contents Original Article
Math. Biol. Bioinf.
2012;7(2):554-566
doi: 10.17537/2012.7.554
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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