voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law,Charity W. Law,Yunshun Chen,Yunshun Chen,Wei Shi,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TLDR
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments, and the voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline.Abstract:
New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.read more
Citations
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Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow
Dominik Buschmann,Anna Haberberger,Benedikt Kirchner,Melanie Spornraft,Irmgard Riedmaier,Gustav Schelling,Michael W. Pfaffl +6 more
TL;DR: Recommendations will encourage better sequencing practice, increase experimental transparency and lead to more reproducible small RNA-Seq results, which will ultimately enhance the validity of biomarker signatures, and allow reliable and robust clinical predictions.
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Caloric restriction disrupts the microbiota and colonization resistance.
Reiner Jumpertz von Schwartzenberg,Jordan E. Bisanz,Svetlana Lyalina,Peter Spanogiannopoulos,Qi Yan Ang,Jingwei Cai,Sophia Dickmann,Marie Friedrich,Su Yang Liu,Stephanie L. Collins,Danielle Ingebrigtsen,Steve Miller,Jessie A. Turnbaugh,Andrew D. Patterson,Katherine S. Pollard,Knut Mai,Joachim Spranger,Peter J. Turnbaugh +17 more
TL;DR: In this article, a randomized human intervention study using a very low-calorie diet (NCT01105143) showed that severe calorie restriction led to a decrease in bacterial abundance and restructuring of the gut microbiome.
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RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis
Koen Van den Berge,Katharina M. Hembach,Charlotte Soneson,Charlotte Soneson,Simone Tiberi,Lieven Clement,Michael I. Love,Rob Patro,Mark D. Robinson +8 more
TL;DR: The measurement of transcriptome-wide gene expression has convincingly shown the ability to describe the activity of individual genes at different levels ofexpression in the genome.
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A biobank of small cell lung cancer CDX models elucidates inter- and intratumoral phenotypic heterogeneity
Kathryn Simpson,Ruth A Stoney,Kristopher K. Frese,Nicole Simms,William Rowe,Simon P. Pearce,Sam Humphrey,Laura Booth,Derrick Morgan,Marek Dynowski,Francesca Trapani,Alessia Catozzi,Mitchell Revill,Thomas Helps,Melanie Galvin,Luc Girard,Daisuke Nonaka,Louise Carter,Matthew G Krebs,Natalie Cook,Mathew Carter,Lynsey Priest,Alastair R.W. Kerr,Adi F. Gazdar,Fiona H Blackhall,Caroline Dive +25 more
TL;DR: A biobank of 38 CDX models, including six CDX pairs generated pretreatment and at disease progression revealing complex intra- and intertumoral heterogeneity is described, which provides a research resource to facilitate SCLC personalized medicine.
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ssGSEA score-based Ras dependency indexes derived from gene expression data reveal potential Ras addiction mechanisms with possible clinical implications.
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References
More filters
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Book
Generalized Linear Models
Peter McCullagh,John A. Nelder +1 more
TL;DR: In this paper, a generalization of the analysis of variance is given for these models using log- likelihoods, illustrated by examples relating to four distributions; the Normal, Binomial (probit analysis, etc.), Poisson (contingency tables), and gamma (variance components).
Journal ArticleDOI
featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features
TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
Journal ArticleDOI
Differential expression analysis for sequence count data.
Simon Anders,Wolfgang Huber +1 more
TL;DR: A method based on the negative binomial distribution, with variance and mean linked by local regression, is proposed and an implementation, DESeq, as an R/Bioconductor package is presented.