Tackling the widespread and critical impact of batch effects in high-throughput data

作者: Jeffrey T Leek , Robert B Scharpf , Héctor Corrada Bravo , David Simcha , Benjamin Langmead

DOI: 10.1038/NRG2825

关键词:

摘要: … SVA estimates the sources of batch effects directly from the high-throughput data so that downstream significance analyses can be corrected. Variables estimated with SVA …

参考文章(27)
Antony Unwin, Chun-Houh Chen, Wolfgang Hädrdle, Handbook of Data Visualization Springer. ,(2016)
Michael J Zilliox, Rafael A Irizarry, A gene expression bar code for microarray data. Nature Methods. ,vol. 4, pp. 911- 913 ,(2007) , 10.1038/NMETH1102
David B. Allison, Xiangqin Cui, Grier P. Page, Mahyar Sabripour, Microarray data analysis: from disarray to consolidation and consensus. Nature Reviews Genetics. ,vol. 7, pp. 55- 65 ,(2006) , 10.1038/NRG1749
Joshua M Akey, Shameek Biswas, Jeffrey T Leek, John D Storey, None, On the design and analysis of gene expression studies in human populations. Nature Genetics. ,vol. 39, pp. 807- 808 ,(2007) , 10.1038/NG0707-807
Keith A. Baggerly, Kevin R. Coombes, E. Shannon Neeley, Run Batch Effects Potentially Compromise the Usefulness of Genomic Signatures for Ovarian Cancer Journal of Clinical Oncology. ,vol. 26, pp. 1186- 1187 ,(2008) , 10.1200/JCO.2007.15.1951
Thomas L. Fare, Ernest M. Coffey, Hongyue Dai, Yudong D. He, Deborah A. Kessler, Kristopher A. Kilian, John E. Koch, Eric LeProust, Matthew J. Marton, Michael R. Meyer, Roland B. Stoughton, George Y. Tokiwa, Yanqun Wang, Effects of atmospheric ozone on microarray data quality. Analytical Chemistry. ,vol. 75, pp. 4672- 4675 ,(2003) , 10.1021/AC034241B
Hsi-Che Liu, Chien-Yu Chen, Yu-Ting Liu, Cheng-Bang Chu, Der-Cherng Liang, Lee-Yung Shih, Chih-Jen Lin, Cross-generation and cross-laboratory predictions of Affymetrix microarrays by rank-based methods Journal of Biomedical Informatics. ,vol. 41, pp. 570- 579 ,(2008) , 10.1016/J.JBI.2007.11.005
TIH Project, None, The International HapMap Project Nature. ,vol. 426, pp. 789- 796 ,(2003) , 10.1038/NATURE02168
R. B. Scharpf, I. Ruczinski, B. Carvalho, B. Doan, A. Chakravarti, R. A. Irizarry, A multilevel model to address batch effects in copy number estimation using SNP arrays Biostatistics. ,vol. 12, pp. 33- 50 ,(2011) , 10.1093/BIOSTATISTICS/KXQ043