swMATH ID: 14376
Software Authors: Troyanskaya, O.; Cantor, M.; Sherlock, G.; Brown, P.; Hastie, T.; Tibshirani, R.; Botstein, D.; Altman, R.
Description: Missing value estimation for DNA microarrays. Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical clustering and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods for imputing missing data are needed, therefore, to minimize the effect of incomplete data sets on analyses, and to increase the range of data sets to which these algorithms can be applied. In this report, we investigate automated methods for estimating missing data. Results: We present a comparative study of several methods for the estimation of missing values in gene microarray data. We implemented and evaluated three methods: a Singular Value Decomposition (SVD) based method (SVDimpute), weighted K-nearest neighbors (KNNimpute), and row average. We evaluated the methods using a variety of parameter settings and over different real data sets, and assessed the robustness of the imputation methods to the amount of missing data over the range of 1–20
Homepage: http://bioinformatics.oxfordjournals.org/content/17/6/520.short
Related Software: R; softImpute; VIM; missForest; MICE; AS 136; UCI-ml; Amelia; glasso; ElemStatLearn; glmnet; rda; Bioconductor; missMDA; Imputation; BaylorEdPsych; MissMech; huge; RegEM; Hmisc
Cited in: 90 Publications
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Cited by 237 Authors

3 Filzmoser, Peter
3 Mazumder, Rahul
3 Simiński, Krzysztof
3 Wasito, Ito
2 Chen, Xiaolin
2 Faisal, Shahla
2 Heun Song, Seuck
2 Hron, Karel
2 Husson, François
2 Josse, Julie
2 Lee, Jaewon
2 Lee, Jungbok
2 Mirkin, Boris G.
2 Park, Mira
2 Speed, Terence Paul
2 Templ, Matthias
2 Tibshirani, Robert John
2 Tutz, Gerhard E.
2 Vanden Branden, Karlien
2 Verboven, Sabine
2 Yang, Aijun
1 Acharjee, Mithun
1 Aghdam, Rosa
1 Alfons, Andreas
1 Allen, Genevera I.
1 Alonso, Andrés M.
1 Annoni, Paola
1 Apostolov, Ognjan
1 Aste, Marco
1 Audigier, Vincent
1 Aziz, Mohammad S.
1 Baaske, Wolfgang E.
1 Bagnoli, Franco
1 Bailey, Rosemary A.
1 Balding, David Joseph
1 Barbiero, Alessandro
1 Barbosa, Susana M.
1 Barhoumi, Rola
1 Ben Brahim, Afef
1 Bertrand, Frédéric
1 Bertsimas, Dimitris John
1 Bhattacharjee, Supritam
1 Bittner, Michael L.
1 Boninsegna, Massimo
1 Bühlmann, Peter
1 Burghardt, Robert C.
1 Carroll, Raymond James
1 Cascone, Marcos Henrique
1 Casleton, Emily
1 Chekouo, Thierry
1 Chen, Chun-Houh
1 Chen, Lifeng
1 Chen, Songxi
1 Chen, Xian
1 Chen, Xiaojing
1 Chen, Yian A.
1 Chen, Zehua
1 Chesney, Thomas
1 Chihara, Laura M.
1 Chou, Chia-Ching
1 Ciccarello, Shannon
1 Crabbe, M. James C.
1 Das, Kumer Pial
1 Das, Swagatam
1 Datta, Shounak
1 Dax, Achiya
1 Di Patti, Francesca
1 DiMaggio, Peter A. jun.
1 Dougherty, Edward R.
1 Du, Zhihua
1 Dudoit, Sandrine
1 Eslahchi, Changiz
1 Faloutsos, Christos
1 Feng, Enmin
1 Ferrari, Pier Alda
1 Filkov, Vladimir
1 Floudas, Christodoulos Achilleus
1 Freno, Antonino
1 Freund, Robert M.
1 Fridlyand, Jane
1 Friedland, Shmuel
1 Frontoni, Emanuele
1 Fu, Tao-Yang
1 Ganjali, Mojtaba
1 Gannoun, Ali
1 García, Eunice Campirán
1 Goldfarb, Donald
1 Goos, Peter
1 Gouveia, Sónia
1 Grigas, Paul
1 Gu, Yu
1 Gunawardena, Harsha P.
1 Gutiérrez-Peña, Eduardo
1 Gygi, Steven P.
1 Hastie, Trevor John
1 He, Ye
1 Heumann, Christian
1 Hilgers, Ralf-Dieter
1 Hotta, Luiz Koodi
1 Hua, Jianping
...and 137 more Authors
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Cited in 51 Serials

7 Computational Statistics and Data Analysis
6 The Annals of Applied Statistics
5 Computational Biology and Chemistry
3 Journal of the American Statistical Association
3 Machine Learning
3 Statistical Applications in Genetics and Molecular Biology
3 Electronic Journal of Statistics
2 Annals of the Institute of Statistical Mathematics
2 Journal of Computational and Applied Mathematics
2 Journal of Multivariate Analysis
2 Journal of Statistical Planning and Inference
2 Computational Statistics
2 Communications in Statistics. Simulation and Computation
2 Pattern Recognition
2 Journal of Applied Statistics
2 Journal of Machine Learning Research (JMLR)
2 Advances in Data Analysis and Classification. ADAC
2 Statistical Analysis and Data Mining
2 Statistics and Computing
1 Mathematical Biosciences
1 Fuzzy Sets and Systems
1 Information Sciences
1 Computers & Operations Research
1 Neural Networks
1 Journal of Global Optimization
1 Applied Mathematical Modelling
1 Communications in Statistics. Theory and Methods
1 Journal of Statistical Computation and Simulation
1 Linear Algebra and its Applications
1 Mathematical Programming. Series A. Series B
1 Foundations of Computing and Decision Sciences
1 SIAM Journal on Optimization
1 Journal of Mathematical Imaging and Vision
1 Statistical Papers
1 Mathematical Problems in Engineering
1 PAA. Pattern Analysis and Applications
1 Data Mining and Knowledge Discovery
1 International Journal of Applied Mathematics and Computer Science
1 Applied Stochastic Models in Business and Industry
1 Quantitative Finance
1 Statistical Methods and Applications
1 Statistical Methodology
1 Signal, Image and Video Processing
1 Journal of Statistical Theory and Practice
1 Mathematical Geosciences
1 Journal de la Société Française de Statistique
1 Sankhyā. Series B
1 Computer Science Review
1 Statistics for Biology and Health
1 Science, Engineering, and Biology Informatics

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