limma powers differential expression analyses for RNA-sequencing and microarray studies

Nucleic Acids Research
Matthew E RitchieGordon K Smyth

Abstract

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possi...Continue Reading

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References

Jan 10, 2002·Genome Research·Reinhard HoffmannFritz Melchers
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Charles KooperbergToshio Tsukiyama
Nov 5, 2003·Methods : a Companion to Methods in Enzymology·Gordon K Smyth, Terry Speed
Aug 7, 2004·Bioinformatics·James M Wettenhall, Gordon K Smyth
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Mar 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Melissa J PeartRicky W Johnstone
Jun 28, 2005·Nucleic Acids Research·Michael PsarrosBeate Sick
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Dec 24, 2005·BMC Bioinformatics·Xiaoqin XiaYipeng Wang
Feb 4, 2006·Bioinformatics·James M WettenhallGordon K Smyth
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Robert Gentleman
May 23, 2006·BMC Bioinformatics·Matthew E RitchieGordon K Smyth
Jul 18, 2006·Nucleic Acids Research·Johannes RainerZlatko Trajanoski
Oct 25, 2006·BMC Bioinformatics·Sophie LemoineStéphane Le Crom
May 23, 2007·Nucleic Acids Research·Hubert RehrauerRalph Schlapbach
Aug 28, 2007·Bioinformatics·Matthew E RitchieGordon K Smyth
Aug 2, 2008·BMC Genomics·Joëlle MichaudHamish S Scott
Nov 27, 2008·Genes & Nutrition·P J De GrootM Müller
Jan 30, 2009·Bioinformatics·Davis J McCarthy, Gordon K Smyth
Mar 7, 2009·The Journal of Immunology : Official Journal of the American Association of Immunologists·François-Xavier HubertHamish S Scott
Jan 9, 2010·Nucleic Acids Research·Wei ShiGordon K Smyth
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Mar 12, 2010·Nature·Joseph K PickrellJonathan K Pritchard
Apr 13, 2010·Nature·Marie-Liesse Asselin-LabatJane E Visvader
Jul 9, 2010·Bioinformatics·Di WuGordon K Smyth
Jul 17, 2010·Bioinformatics·Heiko A MannspergerUlrike Korf
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
May 29, 2012·Nucleic Acids Research·Di Wu, Gordon K Smyth
Apr 6, 2013·Nucleic Acids Research·Yang LiaoWei Shi

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Citations

Jan 6, 2016·Environmental Science & Technology·John R HarleyTodd O'Hara
Feb 2, 2016·Journal of Proteome Research·Rik VerdonckLiliane Schoofs
Mar 17, 2016·Genomics Data·Ruijie LiuMatthew E Ritchie
Oct 2, 2015·Gynecological Endocrinology : the Official Journal of the International Society of Gynecological Endocrinology·Paula B T FettbackPaulo C Serafini
Oct 21, 2015·Genomics Data·Aliaksei Z HolikMarie-Liesse Asselin-Labat
Oct 21, 2015·Genomics Data·Jessica Rodrigues PlaçaWilson Araújo Silva
Feb 16, 2016·Genomics, Proteomics & Bioinformatics·Pingjian Yu, Wei Lin
Mar 5, 2016·Computational Biology and Chemistry·Shila Ghazanfar, Jean Yee Hwa Yang
Feb 14, 2016·Bioinformatics·Victor L JongMarinus J C Eijkemans
Feb 10, 2016·Environmental and Molecular Mutagenesis·Rui XiaoArthur L Penn
Oct 13, 2015·Biochimie·Alejandro Gomez-AuliOliver Schilling
Nov 18, 2015·Cancer Biology & Therapy·Rajani KantetiRavi Salgia
May 15, 2015·Diabetes·Sini HeinonenKirsi H Pietiläinen
Feb 5, 2016·Thrombosis and Haemostasis·Nataly MaimariRob Krams
Feb 24, 2016·Toxicology and Applied Pharmacology·Liliya M FatkhutdinovaAnna A Shvedova
Feb 2, 2016·Epigenetics : Official Journal of the DNA Methylation Society·Sergi Sayols-BaixerasRoberto Elosua
Dec 10, 2015·Epigenetics : Official Journal of the DNA Methylation Society·Semira GonsethJoseph L Wiemels
Aug 31, 2016·Nature Microbiology·Mohammad Tauqeer AlamMarkus Ralser
Mar 15, 2016·Cellular and Molecular Gastroenterology and Hepatology·Jinsheng YuMark J Manary
Dec 9, 2015·Human Molecular Genetics·Carolina Soriano-TárragaUNKNOWN GENESTROKE Consortium
Jan 5, 2016·Nature Neuroscience·Bosiljka TasicHongkui Zeng
Dec 23, 2015·Nature Genetics·Jessica OkosunJude Fitzgibbon
Oct 16, 2015·Proceedings of the National Academy of Sciences of the United States of America·Bryan A SmithOwen N Witte
Dec 19, 2015·The Plant Journal : for Cell and Molecular Biology·Andrew SchneiderEva Collakova

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Datasets Mentioned

BETA
GSE2593
GSE52870

Methods Mentioned

BETA
gene knock-out
RNA-seq
Feature Extraction
PCR

Software Mentioned

lmFit
CarmaWEB
ArrayVision
GenomeStudio
readSpotTypes
BlueFuse
readTargets
counts
plotExons
voom

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