The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy Jr Andr Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker

Data Analysis mathscidoc:1912.43256

Nature biotechnology, 28, (8), 827, 2010.8
Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total,> 30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and
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@inproceedings{leming2010the,
  title={The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models},
  author={Leming Shi, Gregory Campbell, Wendell D Jones, Fabien Campagne, Zhining Wen, Stephen J Walker, Zhenqiang Su, Tzu-Ming Chu, Federico M Goodsaid, Lajos Pusztai, John D Shaughnessy Jr, Andr Oberthuer, Russell S Thomas, Richard S Paules, Mark Fielden, Bart Barlogie, Weijie Chen, Pan Du, Matthias Fischer, Cesare Furlanello, Brandon D Gallas, Xijin Ge, Dalila B Megherbi, W Fraser Symmans, May D Wang, John Zhang, Hans Bitter, Benedikt Brors, Pierre R Bushel, Max Bylesjo, Minjun Chen, Jie Cheng, Jing Cheng, Jeff Chou, Timothy S Davison, Mauro Delorenzi, Youping Deng, Viswanath Devanarayan, David J Dix, Joaquin Dopazo, Kevin C Dorff, Fathi Elloumi, Jianqing Fan, Shicai Fan, Xiaohui Fan, Hong Fang, Nina Gonzaludo, Kenneth R Hess, Huixiao Hong, Jun Huan, Rafael A Irizarry, Richard Judson, Dilafruz Juraeva, Samir Lababidi, Christophe G Lambert, Li Li, Yanen Li, Zhen Li, Simon M Lin, Guozhen Liu, Edward K Lobenhofer, Jun Luo, Wen Luo, Matthew N McCall, Yuri Nikolsky, Gene A Pennello, Roger G Perkins, Reena Philip, Vlad Popovici, Nathan D Price, Feng Qian, Andreas Scherer, Tieliu Shi, Weiwei Shi, Jaeyun Sung, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkata Thodima, Johan Trygg, Lakshmi Vishnuvajjala, Sue Jane Wang, Jianping Wu, Yichao Wu, Qian Xie, Waleed A Yousef, Liang Zhang, Xuegong Zhang, Sheng Zhong, Yiming Zhou, Sheng Zhu, Dhivya Arasappan, Wenjun Bao, Anne Bergstrom Lucas, Frank Berthold, Richard J Brennan, Andreas Buness, Jennifer G Catalano, Chang Chang, Rong Chen, Yiyu Cheng, Jian Cui, Wendy Czika, Francesca Demichelis, Xutao Deng, Damir Dosymbekov, Roland Eils, Yang Feng, Jennifer Fostel, Stephanie Fulmer-Smentek, James C Fuscoe, Laurent Gatto, Weigong Ge, Darlene R Goldstein, Li Guo, Donald N Halbert, Jing Han, Stephen C Harris, Christos Hatzis, Damir Herman, Jianping Huang, Roderick V Jensen, Rui Jiang, Charles D Johnson, Giuseppe Jurman, Yvonne Kahlert, Sadik A Khuder, Matthias Kohl, Jianying Li, Menglong Li, Quan-Zhen Li, Shao Li, Zhiguang Li, Jie Liu, Ying Liu, Zhichao Liu, Lu Meng, Manuel Madera, Francisco Martinez-Murillo, Ignacio Medina, Joseph Meehan, Kelci Miclaus, Richard A Moffitt, David Montaner, Piali Mukherjee, George J Mulligan, Padraic Neville, Tatiana Nikolskaya, Baitang Ning, Grier P Page, and Joel Parker},
  url={http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20191221113316055403816},
  booktitle={Nature biotechnology},
  volume={28},
  number={8},
  pages={827},
  year={2010},
}
Leming Shi, Gregory Campbell, Wendell D Jones, Fabien Campagne, Zhining Wen, Stephen J Walker, Zhenqiang Su, Tzu-Ming Chu, Federico M Goodsaid, Lajos Pusztai, John D Shaughnessy Jr, Andr Oberthuer, Russell S Thomas, Richard S Paules, Mark Fielden, Bart Barlogie, Weijie Chen, Pan Du, Matthias Fischer, Cesare Furlanello, Brandon D Gallas, Xijin Ge, Dalila B Megherbi, W Fraser Symmans, May D Wang, John Zhang, Hans Bitter, Benedikt Brors, Pierre R Bushel, Max Bylesjo, Minjun Chen, Jie Cheng, Jing Cheng, Jeff Chou, Timothy S Davison, Mauro Delorenzi, Youping Deng, Viswanath Devanarayan, David J Dix, Joaquin Dopazo, Kevin C Dorff, Fathi Elloumi, Jianqing Fan, Shicai Fan, Xiaohui Fan, Hong Fang, Nina Gonzaludo, Kenneth R Hess, Huixiao Hong, Jun Huan, Rafael A Irizarry, Richard Judson, Dilafruz Juraeva, Samir Lababidi, Christophe G Lambert, Li Li, Yanen Li, Zhen Li, Simon M Lin, Guozhen Liu, Edward K Lobenhofer, Jun Luo, Wen Luo, Matthew N McCall, Yuri Nikolsky, Gene A Pennello, Roger G Perkins, Reena Philip, Vlad Popovici, Nathan D Price, Feng Qian, Andreas Scherer, Tieliu Shi, Weiwei Shi, Jaeyun Sung, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkata Thodima, Johan Trygg, Lakshmi Vishnuvajjala, Sue Jane Wang, Jianping Wu, Yichao Wu, Qian Xie, Waleed A Yousef, Liang Zhang, Xuegong Zhang, Sheng Zhong, Yiming Zhou, Sheng Zhu, Dhivya Arasappan, Wenjun Bao, Anne Bergstrom Lucas, Frank Berthold, Richard J Brennan, Andreas Buness, Jennifer G Catalano, Chang Chang, Rong Chen, Yiyu Cheng, Jian Cui, Wendy Czika, Francesca Demichelis, Xutao Deng, Damir Dosymbekov, Roland Eils, Yang Feng, Jennifer Fostel, Stephanie Fulmer-Smentek, James C Fuscoe, Laurent Gatto, Weigong Ge, Darlene R Goldstein, Li Guo, Donald N Halbert, Jing Han, Stephen C Harris, Christos Hatzis, Damir Herman, Jianping Huang, Roderick V Jensen, Rui Jiang, Charles D Johnson, Giuseppe Jurman, Yvonne Kahlert, Sadik A Khuder, Matthias Kohl, Jianying Li, Menglong Li, Quan-Zhen Li, Shao Li, Zhiguang Li, Jie Liu, Ying Liu, Zhichao Liu, Lu Meng, Manuel Madera, Francisco Martinez-Murillo, Ignacio Medina, Joseph Meehan, Kelci Miclaus, Richard A Moffitt, David Montaner, Piali Mukherjee, George J Mulligan, Padraic Neville, Tatiana Nikolskaya, Baitang Ning, Grier P Page, and Joel Parker. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. 2010. Vol. 28. In Nature biotechnology. pp.827. http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20191221113316055403816.
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