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Microarray Experiments on Risk Analysis Using R

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Theory and Practice of Risk Assessment

Part of the book series: Springer Proceedings in Mathematics & Statistics ((PROMS,volume 136))

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Abstract

The microarray technique is a powerful biotechnological tool, expanding in a interesting way the vision with which issues in medicine are studied. Microarray technology, allows simultaneous evaluation of the expression of thousands of genes in different tissues of a given organism, and in different stages of development or environmental conditions. However, experiments with microarrays are still substantially costly and laborious, and as a consequence, they are usually conducted with relatively small sample sizes, thereby requiring a careful experimental design and statistical analysis. This paper adopts some applications of microarrays in risk analysis using R statistical software.

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References

  1. Beisser, D., Klau, G., Dandekar, T., Müller, T., Dittrich, T.: BioNet: an R-package for the functional analysis of biological networks. Bioinformatics 26(8), 1129–1130 (2010)

    Article  Google Scholar 

  2. Coffey, C.S., Cofield, S.S.: Parametric linear models. In: Allison, D.B. et al.: DNA Microarrays and Related Genomics Techniques: Design, Analysis, and Interpretation of Experiments. Chap. 12, pp. 223–243, Chapman & Hall/CRC, Boca Raton (2006)

    Google Scholar 

  3. Draghici, S.: Data analysis tools for DNA microarrayus. Chapmann and Hall/CRC Press,Boca Raton (2003)

    Google Scholar 

  4. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K., Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M., Rossini, A.J., Sawitzki, C., Smith, C., Smyth, G., Tierney, L., Yang, J.Y.H., Zhang, J.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80 (2004)

    Google Scholar 

  5. George Casella: Statistical Design. Springer eBooks (2008)

    Google Scholar 

  6. Jaluria, P., Konstantopoulos, K., Betenbaugh, M.: BioNet: a perspective on microarrays: current applications, pitfalls, and potential uses. Microb. Cell Factories 13(8), Article 4 (2007)

    Google Scholar 

  7. Kerr, M.K., Churchill, G.A.: Experimental design for gene expression microarrays. Biostatistics 2, 183–201 (2001)

    Article  MATH  Google Scholar 

  8. Kerr, M.K., Afshari, C.A., Bennett, L., Bushell, P., Martinez, J., Walker, N.J., Churchill, G.A.: A statistical analysis of a gene expression microarray experiment with replication. Statistica Sínica, Taipei 12(2), 203–217 (2002)

    MATH  Google Scholar 

  9. Kitsos, C.P.: Optimal Experimental Design for Non-Linear Models. Springer, Berlin (2013)

    Book  MATH  Google Scholar 

  10. Mora, A., Michalickova, K., Donaldson, I.M.: A survey of protein interaction data and multigenic inherited disorders. BMC Bioinform., 14–47 (2013)

    Google Scholar 

  11. Pramana, S., Lin, D., Haldermans, P., Shkedy, Z., Verbeke, T., Göhlmann, H., Bondt, A., Talloen, W., Bijnens, L.: IsoGene: an R package for analyzing dose-response studies in microarray experiments. R J. 2/1 (2010)

    Google Scholar 

  12. Rosa, G.J.M., Steibel, J.P., Tempelman, R.J.: Reassessing design and analysis of two-colour microarray experiments using mixed effects models. Comp. Funct. Genomics 6(3), 123–131 (2005)

    Article  Google Scholar 

  13. Rosa, G.J.M., Rocha, L.B., Furlan, L.R.: Microarray gene expression studies: experimental design, statistical data analysis, and applications in livestock research. Revista Brasileira de Zootecnia 36, (Special Supplement), 185–209 (2007)

    Google Scholar 

  14. Sacan, A., Ferhatosmanoglu, N., Ferhatosmanoglu, H.: Microarray designer: an online search tool and repository for near-optimal microarray experimental designs. BMC Bioinform. 10, 304–310 (2009)

    Article  Google Scholar 

  15. Sivey, S.D.: Optimal Design. Chapman and Hall, London (1980)

    Google Scholar 

  16. Steibel, J.P., Rosa, G.J.M.: On reference designs for microarray experiments. Stat. Appl. Genet. Mol. Biol. 4(1), Article 36 (2005)

    Google Scholar 

  17. Tempelman, R.J.: Assessing statistical precision, power, and robustness of alternative experimental designs for two color microarray platforms based on mixed effects models. Vet. Immunol. Immunopathol. 105, 175–186 (2005)

    Article  Google Scholar 

  18. Wit, E., Nobile, A., Khanin, R.: Near-optimal designs for dual-channel microarrays studies. Appl. Stat. 54(5), 817–830 (2005)

    MATH  MathSciNet  Google Scholar 

  19. Wolfinger, R.D., Gibson, G., Wolfinger, E.D., Bennet, L., Hamadeh, H., Bushel, P., Afshari, C., Paules, R.S.: Assessing gene significance from cDNA midroarray expression data via mixed models. J. Comput. Biol. 8(6), 625–637 (2009)

    Article  Google Scholar 

  20. Yang, Y.H., Speed, T.: Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3, 579–588 (2002)

    Google Scholar 

  21. Yasrebi, H.: SurvJamda: an R package to predict patients’ survival and risk assessment using joint analysis of microarray gene expression data. Bioinformatics 27(8), 1168–1169 (2011)

    Article  Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge the references for their constructive advices to improve this paper. This research was partially sponsored by national founds through the Fundação Nacional para a Ciência e Tecnologia, Portugal - FCT under the projects (PEst-OE/MAT/UI0006/2011 and PEst-OE/MAT/UI0006/2014).

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Correspondence to Teresa A. Oliveira .

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Oliveira, T.A., Oliveira, A., Monteiro, A.A. (2015). Microarray Experiments on Risk Analysis Using R. In: Kitsos, C., Oliveira, T., Rigas, A., Gulati, S. (eds) Theory and Practice of Risk Assessment. Springer Proceedings in Mathematics & Statistics, vol 136. Springer, Cham. https://doi.org/10.1007/978-3-319-18029-8_12

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