Finding Biomarker Signatures in Pooled Sample Designs : A Simulation Framework for Methodological Comparisons
Joint Authors
Repsilber, Dirk
Telaar, Anna
Nürnberg, Gerd
Source
Issue
Vol. 2010, Issue 2010 (31 Dec. 2010), pp.1-8, 8 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2010-07-04
Country of Publication
Egypt
No. of Pages
8
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Biology
Abstract EN
Detection of discriminating patterns in gene expression data can be accomplished by using various methods of statistical learning.
It has been proposed that sample pooling in this context would have negative effects; however, pooling cannot always be avoided.
We propose a simulation framework to explicitly investigate the parameters of patterns, experimental design, noise, and choice of method in order to find out which effects on classification performance are to be expected.
We use a two-group classification task and simulated gene expression data with independent differentially expressed genes as well as bivariate linear patterns and the combination of both.
Our results show a clear increase of prediction error with pool size.
For pooled training sets powered partial least squares discriminant analysis outperforms discriminance analysis, random forests, and support vector machines with linear or radial kernel for two of three simulated scenarios.
The proposed simulation approach can be implemented to systematically investigate a number of additional scenarios of practical interest.
American Psychological Association (APA)
Telaar, Anna& Nürnberg, Gerd& Repsilber, Dirk. 2010. Finding Biomarker Signatures in Pooled Sample Designs : A Simulation Framework for Methodological Comparisons. Advances in Bioinformatics،Vol. 2010, no. 2010, pp.1-8.
https://search.emarefa.net/detail/BIM-463112
Modern Language Association (MLA)
Telaar, Anna…[et al.]. Finding Biomarker Signatures in Pooled Sample Designs : A Simulation Framework for Methodological Comparisons. Advances in Bioinformatics No. 2010 (2010), pp.1-8.
https://search.emarefa.net/detail/BIM-463112
American Medical Association (AMA)
Telaar, Anna& Nürnberg, Gerd& Repsilber, Dirk. Finding Biomarker Signatures in Pooled Sample Designs : A Simulation Framework for Methodological Comparisons. Advances in Bioinformatics. 2010. Vol. 2010, no. 2010, pp.1-8.
https://search.emarefa.net/detail/BIM-463112
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-463112