limma swMATH ID: 10458 Software Authors: Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK Description: limma: Linear Models for Microarray Data. A survey is given of differential expression analyses using the linear modeling features of the limma package. The chapter starts with the simplest replicated designs and progresses through experiments with two or more groups, direct designs, factorial designs and time course experiments. Experiments with technical as well as biological replication are considered. Empirical Bayes test statistics are explained. The use of quality weights, adaptive background correction and control spots in conjunction with linear modelling is illustrated on the β7 data. Homepage: http://bioconductor.org/packages/release/bioc/html/limma.html Related Software: Bioconductor; gcrma; R; edgeR; Voom; DEseq; sma; GlobalAncova; DESeq2; affy; locfdr; csaw; STRING; TopHat; DAVID; BaySeq; ElemStatLearn; PMA; rattle; GTK+ Cited in: 49 Publications all top 5 Cited by 141 Authors 2 Bar, Haim Y. 2 Nettleton, Dan 2 Schifano, Elizabeth D. 2 Smyth, Gordon K. 1 Alexander, Warren S. 1 Andreassen, Bettina K. 1 Angelini, Claudia 1 Bailey, Trevor C. 1 Bhattacharjee, Atanu 1 Bischl, Bernd 1 Blocker, Alexander W. 1 Bommert, Andrea 1 Booth, James G. 1 Brock, Guy N. 1 Burzykowski, Tomasz 1 Camilier, Isabelle 1 Chen, Jie 1 Chen, Jinggui 1 Cheng, Ruihua 1 Chervoneva, Inna 1 Chiogna, Monica 1 Choi, Dongseok 1 Dasgupta, Nairanjana 1 De Canditiis, Daniela 1 Di, Yanming 1 Djordjilović, Vera 1 Domingo-Relloso, Arce 1 Drăghici, Sorin 1 Du, Chunyan 1 Dunning, Mark J. 1 Evangelista, Daniela 1 Felici, Giovanni 1 Ferkingstad, Egil 1 Frost, H. Robert 1 Gardner-Lubbe, Sugnet 1 Ge, Peng 1 Genz, Alan C. 1 Graf, Alexandra C. 1 Guarracino, Mario Rosario 1 Guo, Zhitang 1 Harbo, Hanne F. 1 Hossain, Ahmed 1 Hu, Jianhua 1 Huang, Guo-Bao 1 Huang, Ping 1 Iglewicz, Boris 1 Jang, Woncheol 1 Jauhari, Shaurya 1 Jeong, Seok-Oh 1 Jiang, Duo 1 Johnson, Marla 1 Juul, Malene 1 Kalina, Jan 1 Ke, Yang 1 Khan, Hafiz Tareq Abdullah 1 Kiihl, Samara F. 1 Klawonn, Frank 1 Kong, Yan 1 Krzanowski, Wojtek Janusz 1 Lang, Michel 1 Langaas, Mette 1 Lazar, Nicole A. 1 le Roux, Niël J. 1 Lee, Stanley 1 Li, Wenxing 1 Liang, Jane W. 1 Lindqvist, Bo Henry 1 Lithio, Andrew 1 Liu, Haibo 1 Liu, Huaping 1 Liu, Xiumin 1 Lun, Aaron T. L. 1 Ma, Yanyuan 1 Madsen, Tobias 1 Majewski, Ian J. 1 Markowetz, Florian 1 Marozzi, Marco 1 Martinez-Garrido, Maria Jose 1 Maunders, H. 1 Meng, Xiaoli 1 Mohammadnejad, Javad 1 Mukherjee, Amitava 1 Mutarelli, Margherita 1 Nguyen, Yet Tien 1 Ni, Fan 1 Niu, Lu 1 Ocaña, Jordi 1 Page, Christian M. 1 Papastamoulis, Panagiotis 1 Parrish, Rudolph S. 1 Pensky, Marianna 1 Phipson, Belinda 1 Posch, Martin 1 Purdom, Elizabeth 1 Rahnenführer, Jörg 1 Rattray, Magnus 1 Razaghi-Moghadam, Zahra 1 Rizvi, S. A. M. 1 Rossell, David 1 Rounge, Trine B. ...and 41 more Authors all top 5 Cited in 27 Serials 8 Statistical Applications in Genetics and Molecular Biology 6 The Annals of Applied Statistics 4 Computational Statistics and Data Analysis 3 Journal of Applied Statistics 3 International Journal of Biomathematics 2 Journal of Multivariate Analysis 2 Journal of Agricultural, Biological, and Environmental Statistics 2 Journal of Theoretical Biology 1 Bulletin of Mathematical Biology 1 Biometrics 1 Journal of Statistical Planning and Inference 1 Kybernetika 1 Statistics & Probability Letters 1 Statistical Science 1 Journal of Global Optimization 1 Statistica Sinica 1 Bernoulli 1 Journal of the Royal Statistical Society. Series B. Statistical Methodology 1 Statistical Modelling 1 REVSTAT 1 Mathematical Biosciences and Engineering 1 Statistical Analysis and Data Mining 1 Electronic Journal of Statistics 1 Journal of Computational and Graphical Statistics 1 Sankhyā. Series B 1 ICSA Book Series in Statistics 1 Chapman & Hall/CRC Mathematical and Computational Biology Series all top 5 Cited in 6 Fields 43 Statistics (62-XX) 30 Biology and other natural sciences (92-XX) 2 Numerical analysis (65-XX) 2 Computer science (68-XX) 2 Operations research, mathematical programming (90-XX) 1 Systems theory; control (93-XX) Citations by Year