A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry

Valkenborg Dirk, Suzy Van Sanden, Lin Dan, Kasim Adetayo, Zhu Qi, Haldermans Philippe, Jansen Ivy, Shkedy Ziv and Burzykowski Tomasz
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Valkenborg Dirk: Hasselt University, Center for Statistics
Suzy Van Sanden: Hasselt University, Center for Statistics
Lin Dan: Hasselt University, Center for Statistics
Kasim Adetayo: Hasselt University, Center for Statistics
Zhu Qi: Hasselt University, Center for Statistics
Haldermans Philippe: Hasselt University, Center for Statistics
Jansen Ivy: Hasselt University, Center for Statistics
Shkedy Ziv: Hasselt University, Center for Statistics
Burzykowski Tomasz: Hasselt University, Center for Statistics

Statistical Applications in Genetics and Molecular Biology, 2008, vol. 7, issue 2, 22

Abstract: We present an approach to construct a classification rule based on the mass spectrometry data provided by the organizers of the "Classification Competition on Clinical Mass Spectrometry Proteomic Diagnosis Data." Before constructing a classification rule, we attempted to pre-process the data and to select features of the spectra that were likely due to true biological signals (i.e., peptides/proteins). As a result, we selected a set of 92 features. To construct the classification rule, we considered eight methods for selecting a subset of the features, combined with seven classification methods. The performance of the resulting 56 combinations was evaluated by using a cross-validation procedure with 1000 re-sampled data sets. The best result, as indicated by the lowest overall misclassification rate, was obtained by using the whole set of 92 features as the input for a support-vector machine (SVM) with a linear kernel. This method was therefore used to construct the classification rule. For the training data set, the total error rate for the classification rule, as estimated by using leave-one-out cross-validation, was equal to 0.16, with the sensitivity and specificity equal to 0.87 and 0.82, respectively.

Keywords: proteomic MALDI-TOFMS preprocessing; feature selection; two-stage cross-validation; classification for clinical diagnosis (search for similar items in EconPapers)
Date: 2008
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Citations: View citations in EconPapers (1)

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DOI: 10.2202/1544-6115.1363

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