SAM swMATH ID: 8356 Software Authors: Storey, John D.; Tibshirani, Robert Description: SAM Thresholding and False Discovery Rates for Detecting Differential Gene Expression in DNA Microarrays. SAM is a computer package for correlating gene expression with an outcome parameter such as treatment, survival time, or diagnostic class. It thresholds an appropriate test statistic and reports the q-value of each test based on a set of sample permutations. SAM works as a Microsoft Excel add-in and has additional features for fold-change thresholding and block permutations. Here, we explain how the SAM methodology works in the context of a general approach to detecting differential gene expression in DNA microarrays. Some recently developed methodology for estimating false discovery rates and q-values has been included in the SAM software, which we summarize here. Homepage: http://rd.springer.com/chapter/10.1007/0-387-21679-0_12 Related Software: Slim; Bioconductor; R; EBarrays; cp4p; GEST; MAANOVA; DESeq2; GitHub; limma; DEseq; Voom; edgeR; sn; ArrayExpress; TM4; WinBUGS; FAMT; FarmTest; TETRAD Cited in: 27 Documents all top 5 Cited by 69 Authors 3 Benjamini, Yoav 3 Biswas, Aniket 3 Parmigiani, Giovanni 3 Tong, Tiejun 2 Beyene, Joseph 2 Chattopadhyay, Gaurangadeb 2 Hossain, Ahmed 2 Yekutieli, Daniel 1 Blades, Natalie J. 1 Blanchard, Gilles 1 Boca, Simina M. 1 Bonassi, Stefano 1 Caffo, Brian S. 1 Céorrada Bravo, Héctor 1 Chatterjee, Aditya 1 Churchill, Gary A. 1 Conlon, Erin Marie 1 Cui, Xiangqin 1 Elmer, Gregory I. 1 Fan, Jianqing 1 Feng, Zeny Z. 1 Garrett, Elizabeth S. 1 Gavrilov, Yulia 1 Gilbert, Peter B. 1 Goldstein, Darlene R. 1 Guerra, Rudy 1 Hastie, Trevor John 1 He, Xuming 1 Hilton, Julia S. 1 Hofman, Jake M. 1 Hu, Pingzhao 1 Hu, Zongliang 1 Hwang, J. T. Gene 1 Irizarry, Rafael A. 1 Jang, Homin 1 Javanmard, Adel 1 Kafkafi, Neri 1 Ke, Yuan 1 Krieger, Abba M. 1 Lee, Norman H. 1 Leek, Jeffrey T. 1 Letwin, Noah E. 1 Li, Gaorong 1 Lovley, Derek R. 1 Methé, Barbara A. 1 Montanari, Andrea 1 Moretti, Stefano 1 Müller, Peter 1 Neuvial, Pierre 1 Nevin, K. P. 1 Patrone, Fioravante 1 Postier, B. L. 1 Qiu, Jing 1 Reiner-Benaim, Anat 1 Robert, Christian P. 1 Roquain, Étienne 1 Rousseau, Judith 1 Sarkar, Sanat Kumar 1 Sharma, Amit Raj 1 Sun, Qiang 1 Tibshirani, Robert John 1 Wang, Huixia 1 Wang, Yuedong 1 Watts, Duncan James 1 Willan, Andrew R. 1 Yang, Yiping 1 Zeger, Scott L. 1 Zhao, Hongyu 1 Zhou, Wen-Xin all top 5 Cited in 19 Serials 4 Journal of Applied Statistics 2 The Annals of Statistics 2 Biometrics 2 Journal of the American Statistical Association 2 Biostatistics 1 Scandinavian Journal of Statistics 1 Biometrika 1 Journal of Multivariate Analysis 1 Statistica Neerlandica 1 Communications in Statistics. Simulation and Computation 1 Computational Statistics and Data Analysis 1 Statistical Papers 1 Top 1 Journal of the Royal Statistical Society. Series C. Applied Statistics 1 Journal of Machine Learning Research (JMLR) 1 Electronic Journal of Statistics 1 The Annals of Applied Statistics 1 Statistics for Biology and Health 1 Chapman & Hall/CRC Mathematical and Computational Biology Series all top 5 Cited in 6 Fields 25 Statistics (62-XX) 8 Biology and other natural sciences (92-XX) 5 Numerical analysis (65-XX) 2 General and overarching topics; collections (00-XX) 1 Probability theory and stochastic processes (60-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) Citations by Year