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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A cell identity switch allows residual BCC to survive Hedgehog pathway inhibition.
Brian Biehs,Gerrit J. P. Dijkgraaf,Robert Piskol,Bruno Alicke,Soufiane Boumahdi,Franklin Peale,Stephen E. Gould,Frederic J. de Sauvage +7 more
TL;DR: Treatment of BCC with both vismodegib and a Wnt pathway inhibitor reduced the residual tumour burden and enhanced differentiation and identified a resistance mechanism in which tumour cells evade treatment by adopting an alternative identity that does not rely on the original oncogenic driver for survival.
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A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data
TL;DR: A binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation are presented to address the challenges of modeling bisulfite sequencing data.
Journal ArticleDOI
DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.
Yafeng Zhu,Lukas M. Orre,Yan Zhou Tran,Georgios Mermelekas,Henrik J. Johansson,Alina Malyutina,Simon Anders,Janne Lehtiö +7 more
TL;DR: DQMS takes into account the inherent dependence of protein variance on the number of PSMs or peptides used for quantification, thereby providing a more accurate variance estimation and achieving better accuracy and statistical power in quantitative proteomics.
Journal ArticleDOI
Cooking shapes the structure and function of the gut microbiome
Rachel N. Carmody,Rachel N. Carmody,Jordan E. Bisanz,Benjamin P. Bowen,Benjamin P. Bowen,Corinne F. Maurice,Corinne F. Maurice,Svetlana Lyalina,Katherine B. Louie,Katherine B. Louie,Daniel Treen,Daniel Treen,Katia S. Chadaideh,Vayu Maini Rekdal,Elizabeth N. Bess,Peter Spanogiannopoulos,Qi Yan Ang,Kylynda C. Bauer,Thomas W. Balon,Katherine S. Pollard,Trent R. Northen,Trent R. Northen,Peter J. Turnbaugh,Peter J. Turnbaugh +23 more
TL;DR: It is shown that a plant diet served raw versus cooked reshapes the murine gut microbiome, with effects attributable to improvements in starch digestibility and degradation of plant-derived compounds and prompt the hypothesis that humans and the authors' microbiomes co-evolved under unique cooking-related pressures.
Journal ArticleDOI
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.
Jarny Choi,Jarny Choi,Tracey M. Baldwin,Mae Wong,Jessica E. Bolden,Jessica E. Bolden,Kirsten A. Fairfax,Kirsten A. Fairfax,Erin C. Lucas,Rebecca Cole,Christine Biben,Christine Biben,Clare Morgan,Clare Morgan,Kerry A. Ramsay,Ashley P. Ng,Ashley P. Ng,Maria Kauppi,Maria Kauppi,Lynn M. Corcoran,Lynn M. Corcoran,Wei Shi,Wei Shi,Nicholas J. Wilson,Michael J. Wilson,Warren S. Alexander,Warren S. Alexander,Douglas J. Hilton,Douglas J. Hilton,Carolyn A. de Graaf,Carolyn A. de Graaf +30 more
TL;DR: Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, is updated to include RNA-seq gene- expression data from both mice and humans, and the ability to compare gene expression across data sets and species is added.
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.