Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods
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Abstract
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DOI: 10.1371/journal.pone.0017238
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References listed on IDEAS
- M. Kathleen Kerr, 2003. "Design Considerations for Efficient and Effective Microarray Studies," Biometrics, The International Biometric Society, vol. 59(4), pages 822-828, December.
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- Xia Qing & Thompson Jeffrey A. & Koestler Devin C., 2021. "Batch effect reduction of microarray data with dependent samples using an empirical Bayes approach (BRIDGE)," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 20(4-6), pages 101-119, December.
- Charlotte Soneson & Sarah Gerster & Mauro Delorenzi, 2014. "Batch Effect Confounding Leads to Strong Bias in Performance Estimates Obtained by Cross-Validation," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-13, June.
- Romain Banchereau & Alejandro Jordan-Villegas & Monica Ardura & Asuncion Mejias & Nicole Baldwin & Hui Xu & Elizabeth Saye & Jose Rossello-Urgell & Phuong Nguyen & Derek Blankenship & Clarence B Creec, 2012. "Host Immune Transcriptional Profiles Reflect the Variability in Clinical Disease Manifestations in Patients with Staphylococcus aureus Infections," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-11, April.
- Qi Su & Qin Liu & Raphaela Iris Lau & Jingwan Zhang & Zhilu Xu & Yun Kit Yeoh & Thomas W. H. Leung & Whitney Tang & Lin Zhang & Jessie Q. Y. Liang & Yuk Kam Yau & Jiaying Zheng & Chengyu Liu & Mengjin, 2022. "Faecal microbiome-based machine learning for multi-class disease diagnosis," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
- Sean M Gibbons & Claire Duvallet & Eric J Alm, 2018. "Correcting for batch effects in case-control microbiome studies," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-17, April.
- Nazifa Ahmed Moumi & Badhan Das & Zarin Tasnim Promi & Nishat Anjum Bristy & Md Shamsuzzoha Bayzid, 2019. "Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data," PLOS ONE, Public Library of Science, vol. 14(9), pages 1-25, September.
- Jacopo Umberto Verga & Matthew Huff & Diarmuid Owens & Bethany J. Wolf & Gary Hardiman, 2022. "Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes," IJERPH, MDPI, vol. 19(1), pages 1-24, January.
- Aline Talhouk & Stefan Kommoss & Robertson Mackenzie & Martin Cheung & Samuel Leung & Derek S Chiu & Steve E Kalloger & David G Huntsman & Stephanie Chen & Maria Intermaggio & Jacek Gronwald & Fong C , 2016. "Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-18, April.
- Raihan K Uddin & Shiva M Singh, 2013. "Hippocampal Gene Expression Meta-Analysis Identifies Aging and Age-Associated Spatial Learning Impairment (ASLI) Genes and Pathways," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-16, July.
- Kejian Wang & Jiazhi Sun & Shufeng Zhou & Chunling Wan & Shengying Qin & Can Li & Lin He & Lun Yang, 2013. "Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-9, November.
- Samir Dou & Nathalie Villa-Vialaneix & Laurence Liaubet & Yvon Billon & Mario Giorgi & Hélène Gilbert & Jean-Luc Gourdine & Juliette Riquet & David Renaudeau, 2017. "1HNMR-Based metabolomic profiling method to develop plasma biomarkers for sensitivity to chronic heat stress in growing pigs," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-18, November.
- Christian Müller & Arne Schillert & Caroline Röthemeier & David-Alexandre Trégouët & Carole Proust & Harald Binder & Norbert Pfeiffer & Manfred Beutel & Karl J Lackner & Renate B Schnabel & Laurence T, 2016. "Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-23, June.
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