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http://hdl.handle.net/1942/8049
Title: | A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry | Authors: | VALKENBORG, Dirk VAN SANDEN, Suzy LIN, Dan KASIM, Adetayo JANSEN, Ivy SHKEDY, Ziv BURZYKOWSKI, Tomasz HALDERMANS, Philippe ZHU, Qi |
Issue Date: | 2008 | Publisher: | BERKELEY ELECTRONIC PRESS | Source: | STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, 7(2) | 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. | Document URI: | http://hdl.handle.net/1942/8049 | ISSN: | 2194-6302 | e-ISSN: | 1544-6115 | ISI #: | 000254568100009 | Category: | A1 | Type: | Journal Contribution | Validations: | ecoom 2009 |
Appears in Collections: | Research publications |
Files in This Item:
File | Description | Size | Format | |
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A Cross-validation Study to Select.pdf | Peer-reviewed author version | 9.02 MB | Adobe PDF | View/Open |
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