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Bioinformatics Advance Access originally published online on August 6, 2009
Bioinformatics 2009 25(20):2708-2714; doi:10.1093/bioinformatics/btp478
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model

Chen Zhang 1, Chunguo Wu 1, Enrico Blanzieri 2,*, You Zhou 1, Yan Wang 1, Wei Du 1 and Yanchun Liang 1,*

1 College of Computer Science and Technology, Jilin University, 130012, China and 2 Department of Information and Communication Technology, University of Trento, 38050 Povo, Italy

* To whom correspondence should be addressed.


  Abstract

Motivation: Mislabeled samples often appear in gene expression profile because of the similarity of different sub-type of disease and the subjective misdiagnosis. The mislabeled samples deteriorate supervised learning procedures. The LOOE-sensitivity algorithm is an approach for mislabeled sample detection for microarray based on data perturbation. However, the failure of measuring the perturbing effect makes the LOOE-sensitivity algorithm a poor performance. The purpose of this article is to design a novel detection method for mislabeled samples of microarray, which could take advantage of the measuring effect of data perturbations.

Results: To measure the effect of data perturbation, we define an index named perturbing influence value (PIV), based on the support vector machine (SVM) regression model. The Column Algorithm (CAPIV), Row Algorithm (RAPIV) and progressive Row Algorithm (PRAPIV) based on the PIV value are proposed to detect the mislabeled samples. Experimental results obtained by using six artificial datasets and five microarray datasets demonstrate that all proposed methods in this article are superior to LOOE-sensitivity. Moreover, compared with the simple SVM and CL-stability, the PRAPIV algorithm shows an increase in precision and high recall.

Availability: The program and source code (in JAVA) are publicly available at http://ccst.jlu.edu.cn/CSBG/PIVS/index.htm

Contact: blanzier{at}dit.unitn.it; ycliang{at}jlu.edu.cn

Associate Editor: Joaquin Dopazo

Received on April 8, 2009; revised on July 14, 2009; accepted on August 3, 2009

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