Correcting for batch effects in case-control microbiome studies
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1006102
Download full text from publisher
References listed on IDEAS
- Claire Duvallet & Sean M. Gibbons & Thomas Gurry & Rafael A. Irizarry & Eric J. Alm, 2017. "Meta-analysis of gut microbiome studies identifies disease-specific and shared responses," Nature Communications, Nature, vol. 8(1), pages 1-10, December.
- Peter J. Turnbaugh & Micah Hamady & Tanya Yatsunenko & Brandi L. Cantarel & Alexis Duncan & Ruth E. Ley & Mitchell L. Sogin & William J. Jones & Bruce A. Roe & Jason P. Affourtit & Michael Egholm & Be, 2009. "A core gut microbiome in obese and lean twins," Nature, Nature, vol. 457(7228), pages 480-484, January.
- Chao Chen & Kay Grennan & Judith Badner & Dandan Zhang & Elliot Gershon & Li Jin & Chunyu Liu, 2011. "Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-10, February.
- Edoardo Pasolli & Duy Tin Truong & Faizan Malik & Levi Waldron & Nicola Segata, 2016. "Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-26, July.
- Jeffrey T Leek & John D Storey, 2007. "Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis," PLOS Genetics, Public Library of Science, vol. 3(9), pages 1-12, September.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Wodan Ling & Jiuyao Lu & Ni Zhao & Anju Lulla & Anna M. Plantinga & Weijia Fu & Angela Zhang & Hongjiao Liu & Hoseung Song & Zhigang Li & Jun Chen & Timothy W. Randolph & Wei Li A. Koay & James R. Whi, 2022. "Batch effects removal for microbiome data via conditional quantile regression," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- 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.
- 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.
- 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.
- 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.
- Alan Le Goallec & Braden T Tierney & Jacob M Luber & Evan M Cofer & Aleksandar D Kostic & Chirag J Patel, 2020. "A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type," PLOS Computational Biology, Public Library of Science, vol. 16(5), pages 1-21, May.
- John Molloy & Katrina Allen & Fiona Collier & Mimi L. K. Tang & Alister C. Ward & Peter Vuillermin, 2013. "The Potential Link between Gut Microbiota and IgE-Mediated Food Allergy in Early Life," IJERPH, MDPI, vol. 10(12), pages 1-22, December.
- Pirjo Wacklin & Harri Mäkivuokko & Noora Alakulppi & Janne Nikkilä & Heli Tenkanen & Jarkko Räbinä & Jukka Partanen & Kari Aranko & Jaana Mättö, 2011. "Secretor Genotype (FUT2 gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine," PLOS ONE, Public Library of Science, vol. 6(5), pages 1-10, May.
- Jaron Thompson & Renee Johansen & John Dunbar & Brian Munsky, 2019. "Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-16, July.
- repec:jss:jstsof:40:i14 is not listed on IDEAS
- Emanuele Aliverti & Kristian Lum & James E. Johndrow & David B. Dunson, 2021. "Removing the influence of group variables in high‐dimensional predictive modelling," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 184(3), pages 791-811, July.
- Seungchul Baek & Yen‐Yi Ho & Yanyuan Ma, 2020. "Using sufficient direction factor model to analyze latent activities associated with breast cancer survival," Biometrics, The International Biometric Society, vol. 76(4), pages 1340-1350, December.
- Griffin, Maryclare & Hoff, Peter D., 2019. "Lasso ANOVA decompositions for matrix and tensor data," Computational Statistics & Data Analysis, Elsevier, vol. 137(C), pages 181-194.
- Sanjeena Subedi & Drew Neish & Stephen Bak & Zeny Feng, 2020. "Cluster analysis of microbiome data by using mixtures of Dirichlet–multinomial regression models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 69(5), pages 1163-1187, November.
- Shinji Fukuda & Yumiko Nakanishi & Eisuke Chikayama & Hiroshi Ohno & Tsuneo Hino & Jun Kikuchi, 2009. "Evaluation and Characterization of Bacterial Metabolic Dynamics with a Novel Profiling Technique, Real-Time Metabolotyping," PLOS ONE, Public Library of Science, vol. 4(3), pages 1-10, March.
- Chee Ho H’ng & Shanika L. Amarasinghe & Boya Zhang & Hojin Chang & Xinli Qu & David R. Powell & Alberto Rosello-Diez, 2024. "Compensatory growth and recovery of cartilage cytoarchitecture after transient cell death in fetal mouse limbs," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Mark Reimers, 2010. "Making Informed Choices about Microarray Data Analysis," PLOS Computational Biology, Public Library of Science, vol. 6(5), pages 1-7, May.
- Antonino Malacrinò & Victoria A Sadowski & Tvisha K Martin & Nathalia Cavichiolli de Oliveira & Ian J Brackett & James D Feller & Kristian J Harris & Orlando Combita Heredia & Rosa Vescio & Alison E B, 2020. "Biological invasions alter environmental microbiomes: A meta-analysis," PLOS ONE, Public Library of Science, vol. 15(10), pages 1-12, October.
- Leek Jeffrey T & Storey John D., 2011. "The Joint Null Criterion for Multiple Hypothesis Tests," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, June.
- Hannah Lees & Jonathan Swann & Simon M Poucher & Jeremy K Nicholson & Elaine Holmes & Ian D Wilson & Julian R Marchesi, 2014. "Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-11, September.
- Nicoló Fusi & Oliver Stegle & Neil D Lawrence, 2012. "Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-9, January.
- Liat Shenhav & Ori Furman & Leah Briscoe & Mike Thompson & Justin D Silverman & Itzhak Mizrahi & Eran Halperin, 2019. "Modeling the temporal dynamics of the gut microbial community in adults and infants," PLOS Computational Biology, Public Library of Science, vol. 15(6), pages 1-21, June.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1006102. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.