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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In vivo partial reprogramming alters age-associated molecular changes during physiological aging in mice
Kristen C. Browder,Pradeep Reddy,Mako Yamamoto,Amin Haghani,Isabel Guillen,Sanjeeb Kumar Sahu,Chao Wang,Yosu Luque,Javier Prieto,Lei Shi,Kensaku Shojima,Tomoaki Hishida,Zijuan Lai,Qingling Li,Feroza K. Choudhury,Weng Wong,Yuxin Liang,Dewakar Sangaraju,Wendy Sandoval,Concepcion Rodriguez Esteban,Estrella Nuñez Delicado,Pedro Guillén García,Michal Pawlak,Jason A. Vander Heiden,Steve Horvath,Heinrich Jasper,Juan Carlos Izpisua Belmonte +26 more
TL;DR: In this paper , the effects of longer-term partial reprogramming in physiologically aging wild-type mice are unknown, however, they performed various long-term part-reprogramming regimens, including different onset timings, during physiological aging.
Journal ArticleDOI
DDX5 plays essential transcriptional and post-transcriptional roles in the maintenance and function of spermatogonia
Julien M. D. Legrand,Julien M. D. Legrand,Ai-Leen Chan,Ai-Leen Chan,Hue M. La,Hue M. La,Fernando J. Rossello,Fernando J. Rossello,Minna-Liisa Änkö,Minna-Liisa Änkö,Frances V. Fuller-Pace,Robin M. Hobbs,Robin M. Hobbs +12 more
TL;DR: An essential role for RNA helicase DDX5 is demonstrated in maintenance of spermatogonia in adults through control of gene transcription plus RNA processing and export and it is shown that Ddx5 is indispensable for male fertility.
Journal ArticleDOI
Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk.
Sara E. Howden,Sean B. Wilson,Ella Groenewegen,Lakshi T. Starks,Thomas A. Forbes,Thomas A. Forbes,Ker Sin Tan,Jessica M. Vanslambrouck,Emily M. Holloway,Yi-Hsien Chen,Sanjay Jain,Jason R. Spence,Melissa H. Little +12 more
TL;DR: In this article, the authors re-analyzed the transcriptional distinction between distal nephron and ureteric epithelium in human fetal kidney, and showed that the distal kidney segment alone displays significant in vitro plasticity and can adopt a uteric tip identity when isolated and cultured in defined conditions.
Posted ContentDOI
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
TL;DR: diffcyt, a new computational framework for differential discovery analyses in these datasets, based on (i) high-resolution clustering and (ii) empirical Bayes moderated tests adapted from transcriptomics is presented.
Journal ArticleDOI
Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size.
Sophie Lamarre,Pierre Frasse,Mohamed Zouine,Delphine Labourdette,Elise Sainderichin,Guojian Hu,Véronique Le Berre-Anton,Mondher Bouzayen,Elie Maza +8 more
TL;DR: It is concluded that the replicate number has a larger impact than the library size on the power of the DE analysis, except for low-expressed genes, for which both parameters seem to have the same impact.
References
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