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Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling

Author

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  • Jiang Wenyu

    (Concordia University)

  • Varma Sudhir

    (Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, National Cancer Institute)

  • Simon Richard

    (Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute)

Abstract

Cross-validation based point estimates of prediction accuracy are frequently reported in microarray class prediction problems. However these point estimates can be highly variable, particularly for small sample numbers, and it would be useful to provide confidence intervals of prediction accuracy.We performed an extensive study of existing confidence interval methods and compared their performance in terms of empirical coverage and width. We developed a bootstrap case cross-validation (BCCV) resampling scheme and defined several confidence interval methods using BCCV with and without bias-correction.The widely used approach of basing confidence intervals on an independent binomial assumption of the leave-one-out cross-validation errors results in serious under-coverage of the true prediction error. Two split-sample based methods previously proposed in the literature tend to give overly conservative confidence intervals. Using BCCV resampling, the percentile confidence interval method was also found to be overly conservative without bias-correction, while the bias corrected accelerated (BCa) interval method of Efron returns substantially anti-conservative confidence intervals. We propose a simple bias reduction on the BCCV percentile interval. The method provides mildly conservative inference under all circumstances studied and outperforms the other methods in microarray applications with small to moderate sample sizes.

Suggested Citation

  • Jiang Wenyu & Varma Sudhir & Simon Richard, 2008. "Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-22, March.
  • Handle: RePEc:bpj:sagmbi:v:7:y:2008:i:1:n:8
    DOI: 10.2202/1544-6115.1322
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    References listed on IDEAS

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    1. Dudoit S. & Fridlyand J. & Speed T. P, 2002. "Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data," Journal of the American Statistical Association, American Statistical Association, vol. 97, pages 77-87, March.
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    1. Goedhart, Jeroen M. & Klausch, Thomas & van de Wiel, Mark A., 2023. "Estimation of predictive performance in high-dimensional data settings using learning curves," Computational Statistics & Data Analysis, Elsevier, vol. 180(C).

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