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Clustering longitudinal profiles using P-splines and mixed effects models applied to time-course gene expression data

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  • Coffey, N.
  • Hinde, J.
  • Holian, E.

Abstract

Longitudinal data is becoming increasingly common and various methods have been developed to analyze this type of data. Profiles from time-course gene expression studies, where cluster analysis plays an important role to identify groups of co-expressed genes over time, are investigated. A number of procedures have been used to cluster time-course gene expression data, however there are many limitations to the techniques previously described. An alternative approach is proposed, which aims to alleviate some of these limitations. The method exploits the connection between the linear mixed effects model and P-spline smoothing to simultaneously smooth the gene expression data to remove any measurement error/noise and cluster the expression profiles using finite mixtures of mixed effects models. This approach has a number of advantages, including decreased computation time and ease of implementation in standard software packages.

Suggested Citation

  • Coffey, N. & Hinde, J. & Holian, E., 2014. "Clustering longitudinal profiles using P-splines and mixed effects models applied to time-course gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 14-29.
    • Handle: RePEc:eee:csdana:v:71:y:2014:i:c:p:14-29
    DOI: 10.1016/j.csda.2013.04.001
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    1. Ruppert,David & Wand,M. P. & Carroll,R. J., 2003. "Semiparametric Regression," Cambridge Books, Cambridge University Press, number 9780521785167, October.
    2. Li-Xuan Qin & Steven G. Self, 2006. "The Clustering of Regression Models Method with Applications in Gene Expression Data," Biometrics, The International Biometric Society, vol. 62(2), pages 526-533, June.
    3. Lawrence Hubert & Phipps Arabie, 1985. "Comparing partitions," Journal of Classification, Springer;The Classification Society, vol. 2(1), pages 193-218, December.
    4. McLachlan, G. J. & Peel, D. & Bean, R. W., 2003. "Modelling high-dimensional data by mixtures of factor analyzers," Computational Statistics & Data Analysis, Elsevier, vol. 41(3-4), pages 379-388, January.
    5. George C. Tseng & Wing H. Wong, 2005. "Tight Clustering: A Resampling-Based Approach for Identifying Stable and Tight Patterns in Data," Biometrics, The International Biometric Society, vol. 61(1), pages 10-16, March.
    6. Tarpey, Thaddeus, 2007. "Linear Transformations and the k-Means Clustering Algorithm: Applications to Clustering Curves," The American Statistician, American Statistical Association, vol. 61, pages 34-40, February.
    7. Ma, Ping & Zhong, Wenxuan, 2008. "Penalized Clustering of Large-Scale Functional Data With Multiple Covariates," Journal of the American Statistical Association, American Statistical Association, vol. 103, pages 625-636, June.
    8. Mitsunori Kayano & Koji Dozono & Sadanori Konishi, 2010. "Functional Cluster Analysis via Orthonormalized Gaussian Basis Expansions and Its Application," Journal of Classification, Springer;The Classification Society, vol. 27(2), pages 211-230, September.
    9. James G.M. & Sugar C.A., 2003. "Clustering for Sparsely Sampled Functional Data," Journal of the American Statistical Association, American Statistical Association, vol. 98, pages 397-408, January.
    10. Ruppert,David & Wand,M. P. & Carroll,R. J., 2003. "Semiparametric Regression," Cambridge Books, Cambridge University Press, number 9780521780506, October.
    11. Christian Hennig, 2010. "Methods for merging Gaussian mixture components," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 4(1), pages 3-34, April.
    12. Fraley C. & Raftery A.E., 2002. "Model-Based Clustering, Discriminant Analysis, and Density Estimation," Journal of the American Statistical Association, American Statistical Association, vol. 97, pages 611-631, June.
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    Cited by:

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    2. Yupeng Wang & Jianghui Cai & Haifeng Yang & Jie Wang & Bo Liang & Xujun Zhao, 2024. "A New Composite Dissimilarity Measure for Planar Curves Based on Higher-Order Derivatives," Mathematics, MDPI, vol. 12(19), pages 1-17, October.
    3. Tsubasa Ito & Shonosuke Sugasawa, 2023. "Grouped generalized estimating equations for longitudinal data analysis," Biometrics, The International Biometric Society, vol. 79(3), pages 1868-1879, September.
    4. Fang, Kuangnan & Chen, Yuanxing & Ma, Shuangge & Zhang, Qingzhao, 2022. "Biclustering analysis of functionals via penalized fusion," Journal of Multivariate Analysis, Elsevier, vol. 189(C).
    5. Rhoden, Imke & Weller, Daniel & Voit, Ann-Katrin, 2021. "Spatio-temporal dynamics of European innovation: An exploratory approach via multivariate functional data cluster analysis," Ruhr Economic Papers 926, RWI - Leibniz-Institut für Wirtschaftsforschung, Ruhr-University Bochum, TU Dortmund University, University of Duisburg-Essen.

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