Optimal classification for time-course gene expression data using functional data analysis

Joon Jin Song, Weiguo Deng, Ho Jin Lee, Deukwoo Kwon

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

Classification problems have received considerable attention in biological and medical applications. In particular, classification methods combining to microarray technology play an important role in diagnosing and predicting disease, such as cancer, in medical research. Primary objective in classification is to build an optimal classifier based on the training sample in order to predict unknown class in the test sample. In this paper, we propose a unified approach for optimal gene classification with conjunction with functional principal component analysis (FPCA) in functional data analysis (FNDA) framework to classify time-course gene expression profiles based on information from the patterns. To derive an optimal classifier in FNDA, we also propose to find optimal number of bases in the smoothing step and functional principal components in FPCA using a cross-validation technique, and compare the performance of some popular classification techniques in the proposed setting. We illustrate the propose method with a simulation study and a real world data analysis.

Original languageEnglish (US)
Pages (from-to)426-432
Number of pages7
JournalComputational Biology and Chemistry
Volume32
Issue number6
DOIs
StatePublished - Dec 2008
Externally publishedYes

Keywords

  • Classification
  • Functional data analysis
  • Functional principal component analysis
  • Time-course gene expression

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

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