Competition on Clinical Mass Spectrometry Based Proteomic Diagnosis
Introduction
Guest Editor, Bart Mertens, Leiden University Medical Centre
This special issue of Statistical Applications in Genetics and Molecular Biology uses an unusual format in order to provide an insider's perspective on biostatistics research. We present the design, analysis and results of an international competition on mass spectrometry proteomic diagnosis, organized at the Leiden University Medical Centre in The Netherlands. For this collaborative data analysis project , we gave an experimental data set to invited participants, and asked them to construct a diagnostic classification rule for allocation of future patients. The first section of this issue introduces the project, and the second section of the issue describes each participants' analyses. The participants all met in March 2007 to discuss their results, which we will publish later this year in a third section, along with an analysis by David Hand.
Editorial
Introduction to the Competition and Description of the Experiment
Case-Control Breast Cancer Study of MALDI-TOF Proteomic Mass Spectrometry Data on Serum Samples
Martijn P. J. van der Werff, Bart Mertens, Mirre E. de Noo, Marco R. Bladergroen, Hans C. Dalebout, Rob A. E. M. Tollenaar, and Andre M. Deelder
Competition Entry Papers
Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls
Jennifer H. Barrett and David A. Cairns
Developing a Discrimination Rule between Breast Cancer Patients and Controls Using Proteomics Mass Spectrometric Data: A Three-Step Approach
A. Geert Heidema and Nico Nagelkerke
A Classification Model for the Leiden Proteomics Competition
Huub C. J. Hoefsloot, Suzanne Smit, and Age K. Smilde
Empirical Bayes Logistic Regression
Foteini Strimenopoulou and Philip J. Brown
Support Vector Machine Approach to Separate Control and Breast Cancer Serum Samples
Thang V. Pham, Mark A. van de Wiel, and Connie R. Jimenez
A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry
Dirk Valkenborg, Suzy Van Sanden, Dan Lin, Adetayo Kasim, Qi Zhu, Philippe Haldermans, Ivy Jansen, Ziv Shkedy, and Tomasz Burzykowski
Clinical Mass Spectrometry Proteomic Diagnosis by Conformal Predictors
Alex Gammerman, Ilia Nouretdinov, Brian Burford, Alexey Chervonenkis, Vladimir Vovk, and Zhiyuan Luo