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Ridge regression and its applications in genetic studies

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  • M Arashi
  • M Roozbeh
  • N A Hamzah
  • M Gasparini

Abstract

With the advancement of technology, analysis of large-scale data of gene expression is feasible and has become very popular in the era of machine learning. This paper develops an improved ridge approach for the genome regression modeling. When multicollinearity exists in the data set with outliers, we consider a robust ridge estimator, namely the rank ridge regression estimator, for parameter estimation and prediction. On the other hand, the efficiency of the rank ridge regression estimator is highly dependent on the ridge parameter. In general, it is difficult to provide a satisfactory answer about the selection for the ridge parameter. Because of the good properties of generalized cross validation (GCV) and its simplicity, we use it to choose the optimum value of the ridge parameter. The GCV function creates a balance between the precision of the estimators and the bias caused by the ridge estimation. It behaves like an improved estimator of risk and can be used when the number of explanatory variables is larger than the sample size in high-dimensional problems. Finally, some numerical illustrations are given to support our findings.

Suggested Citation

  • M Arashi & M Roozbeh & N A Hamzah & M Gasparini, 2021. "Ridge regression and its applications in genetic studies," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-17, April.
    • Handle: RePEc:plo:pone00:0245376
    DOI: 10.1371/journal.pone.0245376
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    References listed on IDEAS

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    1. Fan J. & Li R., 2001. "Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1348-1360, December.
    2. Roozbeh, Mahdi, 2018. "Optimal QR-based estimation in partially linear regression models with correlated errors using GCV criterion," Computational Statistics & Data Analysis, Elsevier, vol. 117(C), pages 45-61.
    3. Roozbeh, Mahdi, 2016. "Robust ridge estimator in restricted semiparametric regression models," Journal of Multivariate Analysis, Elsevier, vol. 147(C), pages 127-144.
    4. Amini, Morteza & Roozbeh, Mahdi, 2015. "Optimal partial ridge estimation in restricted semiparametric regression models," Journal of Multivariate Analysis, Elsevier, vol. 136(C), pages 26-40.
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