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Unwanted variation, including hidden confounding, is a well-known problem in many fields, particularly large-scale gene expression studies.
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Joe Lucas, Carlos Carvalho, Quanli Wang, Andrea Bild, JR Nevins, and Mike West · 2006
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Principal components analysis corrects for stratification in genome-wide association studies
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Joshua M Akey, Shameek Biswas, Jeffrey T Leek, and John D Storey · 2007
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Adjusting batch effects in microarray expression data using empirical Bayes methods
W Evan Johnson, Cheng Li, and Ariel Rabinovic · 2007
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Jeffrey T Leek and John D Storey · 2007
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Carlos M. Carvalho, Jeffrey Chang, Joseph E. Lucas, Joseph R. Nevins, Quanli Wang, and Mike West · 2008
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Bradley Efron · 2008
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Greg Gibson · 2008
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A general framework for multiple testing dependence
Jeffrey T Leek and John D Storey · 2008
Statistical analysis of factor models of high dimension
Jushan Bai and Kunpeng Li · 2012
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Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies
Nicoló Fusi, Oliver Stegle, and Neil D Lawrence · 2012
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Using control genes to correct for unwanted variation in microarray data
Johann A Gagnon-Bartsch and Terence P Speed · 2012
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Daniel J Stekhoven and Peter Bühlmann · 2012
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Yunting Sun, Nancy R. Zhang, and Art B. Owen · 2012
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Flexible Imputation of Missing Data
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Accounting for non-genetic factors improves the power of eqtl studies
Oliver Stegle, Anitha Kannan, Richard Durbin, and John Winn · 2008
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A factor model approach to multiple testing under dependence
Chloé Friguet, Maela Kloareg, and David Causeur · 2009
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Default prior distributions and efficient posterior computation in Bayesian factor analysis
Joyee Ghosh and David B Dunson · 2009
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Bi-cross-validation of the SVD and the nonnegative matrix factorization
Art B. Owen and Patrick O. Perry · 2009
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Genevera I Allen and Robert Tibshirani · 2010
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Stef van Buuren · 2012
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A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Guillemette Marot, David Castel, Jordi Estelle, et al · 2013
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Human housekeeping genes, revisited
Eli Eisenberg and Erez Y Levanon · 2013
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Removing unwanted variation from high dimensional data with negative controls
Johann Gagnon-Bartsch, Laurent Jacob, and Terence Speed · 2013
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Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge
Sara Mostafavi, Alexis Battle, Xiaowei Zhu, Alexander E Urban, Douglas Levinson, Stephen B Montgomery, and Daphne Koller · 2013
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Degrees of freedom for combining regression with factor analysis
Patrick O Perry and Natesh S Pillai · 2013
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Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping
Can Yang, Lin Wang, Shuqin Zhang, and Hongyu Zhao · 2013
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ruv: Detect and Remove Unwanted Variation using Negative Controls , 2015
Johann Gagnon-Bartsch · 2015
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A reanalysis of mouse encode comparative gene expression data
Yoav Gilad and Orna Mizrahi-Man · 2015
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The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
GTEx Consortium · 2015
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Excess false positive rates in methods for differential gene expression analysis using RNA-seq data
David M Rocke, Luyao Ruan, Yilun Zhang, J. Jared Gossett, Blythe Durbin-Johnson, and Sharon Aviran · 2015
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cate: High Dimensional Factor Analysis and Confounder Adjusted Testing and Estimation , 2015
Jingshu Wang and Qingyuan Zhao · 2015
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Confounder adjustment in multiple hypothesis testing
Jingshu Wang, Qingyuan Zhao, Trevor Hastie, and Art B Owen · 2015
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Normalization of single cell RNA sequencing data using both control and target genes
Mengjie Chen and Xiang Zhou · 2016
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denoiseR: A package for low rank matrix estimation
Julie Josse, Sylvain Sardy, and Stefan Wager · 2016
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sva: Surrogate Variable Analysis , 2016
Jeffrey T. Leek, W. Evan Johnson, Hilary S. Parker, Elana J. Fertig, Andrew E. Jaffe, and John D. Storey · 2016
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Order-invariant prior specification in Bayesian factor analysis
Dennis Leung and Mathias Drton · 2016
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Bi-cross-validation for factor analysis
Art B. Owen and Jingshu Wang · 2016
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False discovery rates: a new deal
Matthew Stephens · 2016
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