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Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

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Cited by:

  1. Wang, Ke & Franks, Alexander & Oh, Sang-Yun, 2023. "Learning Gaussian graphical models with latent confounders," Journal of Multivariate Analysis, Elsevier, vol. 198(C).
  2. Yuto Hasegawa & Juhyun Kim & Gianluca Ursini & Yan Jouroukhin & Xiaolei Zhu & Yu Miyahara & Feiyi Xiong & Samskruthi Madireddy & Mizuho Obayashi & Beat Lutz & Akira Sawa & Solange P. Brown & Mikhail V, 2023. "Microglial cannabinoid receptor type 1 mediates social memory deficits in mice produced by adolescent THC exposure and 16p11.2 duplication," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  3. Zhang, Lyuou & Zhou, Wen & Wang, Haonan, 2021. "A semiparametric latent factor model for large scale temporal data with heteroscedasticity," Journal of Multivariate Analysis, Elsevier, vol. 186(C).
  4. Farnoosh Abbas-Aghababazadeh & Qian Li & Brooke L Fridley, 2018. "Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-21, October.
  5. Zhaohui Qin & Ben Li & Karen N. Conneely & Hao Wu & Ming Hu & Deepak Ayyala & Yongseok Park & Victor X. Jin & Fangyuan Zhang & Han Zhang & Li Li & Shili Lin, 2016. "Statistical Challenges in Analyzing Methylation and Long-Range Chromosomal Interaction Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(2), pages 284-309, October.
  6. Fernando Anjos-Afonso & Florian Buettner & Syed A. Mian & Hefin Rhys & Jimena Perez-Lloret & Manuel Garcia-Albornoz & Namrata Rastogi & Linda Ariza-McNaughton & Dominique Bonnet, 2022. "Single cell analyses identify a highly regenerative and homogenous human CD34+ hematopoietic stem cell population," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  7. Stephen Salerno Jr. & Mahya Mehrmohamadi & Maria V Liberti & Muting Wan & Martin T Wells & James G Booth & Jason W Locasale, 2017. "RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards," PLOS ONE, Public Library of Science, vol. 12(6), pages 1-19, June.
  8. Zemin Zheng & Jinchi Lv & Wei Lin, 2021. "Nonsparse Learning with Latent Variables," Operations Research, INFORMS, vol. 69(1), pages 346-359, January.
  9. 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.
  10. 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.
  11. Chuan Gao & Ian C McDowell & Shiwen Zhao & Christopher D Brown & Barbara E Engelhardt, 2016. "Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-39, July.
  12. Arjun Bhattacharya & Anastasia N. Freedman & Vennela Avula & Rebeca Harris & Weifang Liu & Calvin Pan & Aldons J. Lusis & Robert M. Joseph & Lisa Smeester & Hadley J. Hartwell & Karl C. K. Kuban & Car, 2022. "Placental genomics mediates genetic associations with complex health traits and disease," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  13. Sudhir Varma, 2020. "Blind estimation and correction of microarray batch effect," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-15, April.
  14. Blum Yuna & Houée-Bigot Magalie & Causeur David, 2016. "Sparse factor model for co-expression networks with an application using prior biological knowledge," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(3), pages 253-272, June.
  15. Zachary R. McCaw & Sheila M. Gaynor & Ryan Sun & Xihong Lin, 2023. "Leveraging a surrogate outcome to improve inference on a partially missing target outcome," Biometrics, The International Biometric Society, vol. 79(2), pages 1472-1484, June.
  16. Mark Reimers, 2010. "Making Informed Choices about Microarray Data Analysis," PLOS Computational Biology, Public Library of Science, vol. 6(5), pages 1-7, May.
  17. Angela Tung & Megan M. Sperry & Wesley Clawson & Ananya Pavuluri & Sydney Bulatao & Michelle Yue & Ramses Martinez Flores & Vaibhav P. Pai & Patrick McMillen & Franz Kuchling & Michael Levin, 2024. "Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  18. Friguet, Chloé & Causeur, David, 2011. "Estimation of the proportion of true null hypotheses in high-dimensional data under dependence," Computational Statistics & Data Analysis, Elsevier, vol. 55(9), pages 2665-2676, September.
  19. Robin Gradin & Malin Lindstedt & Henrik Johansson, 2019. "Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects," PLOS ONE, Public Library of Science, vol. 14(2), pages 1-15, February.
  20. Jonathan M. Dreyfuss & Yixing Yuchi & Xuehong Dong & Vissarion Efthymiou & Hui Pan & Donald C. Simonson & Ashley Vernon & Florencia Halperin & Pratik Aryal & Anish Konkar & Yinong Sebastian & Brandon , 2021. "High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  21. 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.
  22. repec:jss:jstsof:40:i14 is not listed on IDEAS
  23. Xuemeng Zhou & Tsz Wing Sam & Ah Young Lee & Danny Leung, 2021. "Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
  24. Michael W Nagle & Jeanne C Latourelle & Adam Labadorf & Alexandra Dumitriu & Tiffany C Hadzi & Thomas G Beach & Richard H Myers, 2016. "The 4p16.3 Parkinson Disease Risk Locus Is Associated with GAK Expression and Genes Involved with the Synaptic Vesicle Membrane," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-14, August.
  25. Sek Won Kong & Christin D Collins & Yuko Shimizu-Motohashi & Ingrid A Holm & Malcolm G Campbell & In-Hee Lee & Stephanie J Brewster & Ellen Hanson & Heather K Harris & Kathryn R Lowe & Adrianna Saada , 2012. "Characteristics and Predictive Value of Blood Transcriptome Signature in Males with Autism Spectrum Disorders," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-13, December.
  26. Parker Hilary S. & Leek Jeffrey T., 2012. "The practical effect of batch on genomic prediction," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-22, April.
  27. Won Jun Lee & Sang Cheol Kim & Jung-Ho Yoon & Sang Jun Yoon & Johan Lim & You-Sun Kim & Sung Won Kwon & Jeong Hill Park, 2016. "Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis," PLOS ONE, Public Library of Science, vol. 11(2), pages 1-20, February.
  28. Kynon J. M. Benjamin & Ria Arora & Arthur S. Feltrin & Geo Pertea & Hunter H. Giles & Joshua M. Stolz & Laura D’Ignazio & Leonardo Collado-Torres & Joo Heon Shin & William S. Ulrich & Thomas M. Hyde &, 2024. "Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  29. Harshita Dogra & Shengxian Ding & Miyeon Yeon & Rongjie Liu & Chao Huang, 2023. "Confounder Adjustment in Shape-on-Scalar Regression Model: Corpus Callosum Shape Alterations in Alzheimer’s Disease," Stats, MDPI, vol. 6(4), pages 1-10, September.
  30. Christos Miliotis & Yuling Ma & Xanthi-Lida Katopodi & Dimitra Karagkouni & Eleni Kanata & Kaia Mattioli & Nikolas Kalavros & Yered H. Pita-Juárez & Felipe Batalini & Varune R. Ramnarine & Shivani Nan, 2024. "Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  31. 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.
  32. Oliver Stegle & Leopold Parts & Richard Durbin & John Winn, 2010. "A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies," PLOS Computational Biology, Public Library of Science, vol. 6(5), pages 1-11, May.
  33. Narasimhan, Balasubramanian & Rubin, Daniel L. & Gross, Samuel M. & Bendersky, Marina & Lavori, Philip W., 2017. "Software for Distributed Computation on Medical Databases: A Demonstration Project," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 77(i13).
  34. 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.
  35. 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.
  36. Jin Hyun Ju & Sushila A Shenoy & Ronald G Crystal & Jason G Mezey, 2017. "An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci," PLOS Computational Biology, Public Library of Science, vol. 13(5), pages 1-26, May.
  37. Miecznikowski, Jeffrey C. & Gold, David & Shepherd, Lori & Liu, Song, 2011. "Deriving and comparing the distribution for the number of false positives in single step methods to control k-FWER," Statistics & Probability Letters, Elsevier, vol. 81(11), pages 1695-1705, November.
  38. Marron, J.S., 2017. "Big Data in context and robustness against heterogeneity," Econometrics and Statistics, Elsevier, vol. 2(C), pages 73-80.
  39. 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.
  40. 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.
  41. Gao Wang & Abhishek Sarkar & Peter Carbonetto & Matthew Stephens, 2020. "A simple new approach to variable selection in regression, with application to genetic fine mapping," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 82(5), pages 1273-1300, December.
  42. 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.
  43. Yunfeng Li & Jarrett Morrow & Benjamin Raby & Kelan Tantisira & Scott T Weiss & Wei Huang & Weiliang Qiu, 2017. "Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data," PLOS ONE, Public Library of Science, vol. 12(3), pages 1-16, March.
  44. Jonathan M Carlson & Zabrina L Brumme & Christine M Rousseau & Chanson J Brumme & Philippa Matthews & Carl Kadie & James I Mullins & Bruce D Walker & P Richard Harrigan & Philip J R Goulder & David He, 2008. "Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag," PLOS Computational Biology, Public Library of Science, vol. 4(11), pages 1-23, November.
  45. 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.
  46. Thilde Terkelsen & Anders Krogh & Elena Papaleo, 2020. "CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data," PLOS Computational Biology, Public Library of Science, vol. 16(3), pages 1-20, March.
  47. Kaido Lepik & Tarmo Annilo & Viktorija Kukuškina & eQTLGen Consortium & Kai Kisand & Zoltán Kutalik & Pärt Peterson & Hedi Peterson, 2017. "C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis," PLOS Computational Biology, Public Library of Science, vol. 13(9), pages 1-20, September.
  48. repec:jss:jstsof:40:i12 is not listed on IDEAS
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