An approach for normalization and quality control for NanoString RNA expression data.
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Arjun Bhattacharya | Mark P Purdue | Michael I Love | Alina M Hamilton | Helena Furberg | Eugene Pietzak | Melissa A Troester | Katherine A Hoadley
[1] A Graham Pockley,et al. Tumor- and cytokine-primed human natural killer cells exhibit distinct phenotypic and transcriptional signatures , 2019, PloS one.
[2] F. Markowetz,et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.
[3] S. Dudoit,et al. Normalization of RNA-seq data using factor analysis of control genes or samples , 2014, Nature Biotechnology.
[4] P. M. Galetti,et al. Genetic Pattern and Demographic History of Salminus brasiliensis: Population Expansion in the Pantanal Region during the Pleistocene , 2018, Front. Genet..
[5] N. Mantel. The detection of disease clustering and a generalized regression approach. , 1967, Cancer research.
[6] Tianye Jia,et al. A Robust Statistical Method for Association-Based eQTL Analysis , 2011, PloS one.
[7] A. Stromberg,et al. NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data , 2016, Nucleic acids research.
[8] Andrey A. Shabalin,et al. Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..
[9] Patrick Breheny,et al. p-Value Histograms: Inference and Diagnostics , 2018, High-throughput.
[10] Philippe Froguel,et al. NACHO: an R package for quality control of NanoString nCounter data , 2020, Bioinform..
[11] G. Shukla,et al. Housekeeping Gene Selection Advisory: Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) and β-Actin Are Targets of miR-644a , 2012, PloS one.
[12] P. Rousseeuw. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis , 1987 .
[13] R. Tibshirani,et al. Repeated observation of breast tumor subtypes in independent gene expression data sets , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[14] C. Perou,et al. Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series , 2019, BMC Genomics.
[15] Sandrine Dudoit,et al. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.
[16] Zhiyuan Hu,et al. Racial Differences in PAM50 Subtypes in the Carolina Breast Cancer Study , 2018, Journal of the National Cancer Institute.
[17] Nicola J. Rinaldi,et al. Genetic effects on gene expression across human tissues , 2017, Nature.
[18] Melissa A. Troester,et al. Race-associated biological differences among Luminal A breast tumors , 2015, Breast Cancer Research and Treatment.
[19] Gábor J. Székely,et al. The Energy of Data , 2017 .
[20] Guolong Zhang,et al. Butyrate Enhances Disease Resistance of Chickens by Inducing Antimicrobial Host Defense Peptide Gene Expression , 2011, PloS one.
[21] E. Mardis,et al. Development and verification of the PAM50-based Prosigna breast cancer gene signature assay , 2015, BMC Medical Genomics.
[22] A. Nobel,et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[23] Christian A. Rees,et al. Molecular portraits of human breast tumours , 2000, Nature.
[24] W. Marston Linehan,et al. Von Hippel-Lindau (VHL) Inactivation in Sporadic Clear Cell Renal Cancer: Associations with Germline VHL Polymorphisms and Etiologic Risk Factors , 2011, PLoS genetics.
[25] Paul C. Boutros,et al. NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data , 2012, Bioinform..
[26] Chaeyoung Lee,et al. Genome-Wide Expression Quantitative Trait Loci Analysis Using Mixed Models , 2018, Front. Genet..
[27] Terence P Speed,et al. A new normalization for Nanostring nCounter gene expression data , 2019, Nucleic acids research.
[28] Beth Newman,et al. Comparative Analysis of Breast Cancer Risk Factors among African-American Women and White Women , 2005 .
[29] Rafael A Irizarry,et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.
[30] Anthony Rhodes,et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. , 2010, Archives of pathology & laboratory medicine.
[31] William N. Venables,et al. Modern Applied Statistics with S , 2010 .
[32] L. S. Callahan,et al. Gradient Material Strategies for Hydrogel Optimization in Tissue Engineering Applications. , 2018 .
[33] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[34] Terence P. Speed,et al. Systematic noise degrades gene co-expression signals but can be corrected , 2015, BMC Bioinformatics.
[35] Zhonghu Bai,et al. Cancer Hallmarks, Biomarkers and Breast Cancer Molecular Subtypes , 2016, Journal of Cancer.
[36] Arjun Bhattacharya,et al. A framework for transcriptome-wide association studies in breast cancer in diverse study populations , 2020, Genome Biology.
[37] Richard W Titball,et al. Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups , 2019, BMC Genomics.
[38] Peter W. Laird,et al. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer , 2018, Cell.
[39] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[40] P Boffetta,et al. Tobacco smoking, body mass index, hypertension, and kidney cancer risk in central and eastern Europe , 2008, British Journal of Cancer.
[41] F. Speleman,et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.
[42] Alan Sharpe,et al. High-Frequency Targetable EGFR Mutations in Sinonasal Squamous Cell Carcinomas Arising from Inverted Sinonasal Papilloma. , 2015, Cancer research.
[43] Jennifer L. Osborn,et al. Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.
[44] Johann A. Gagnon-Bartsch,et al. Using control genes to correct for unwanted variation in microarray data. , 2012, Biostatistics.
[45] Matthias Kohl,et al. ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data , 2012, BMC Genomics.
[46] R. Barber,et al. GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. , 2005, Physiological genomics.
[47] Chun Jimmie Ye,et al. Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots , 2008, Genetics.
[48] André F. Vieira,et al. An Update on Breast Cancer Multigene Prognostic Tests—Emergent Clinical Biomarkers , 2018, Front. Med..
[49] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .
[50] Wei Lu,et al. RCRnorm: An integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data. , 2019, The annals of applied statistics.