Bioinformatics Vol. 17 no. 6 2001
Pages 520-525
© 2001 Oxford University Press
Missing value estimation methods for DNA microarrays
1 Stanford Medical Informatics
2 Department of Genetics, Stanford
University School of Medicine, Stanford, CA, USA
3 Department of Biochemistry, Stanford
University School of Medicine, and Howard Hughes Medical Institute,
Stanford, CA, USA
4 Departments of Statistics and Health
Research and Policy, Stanford University, Stanford, CA, USA
Received on November 13, 2000
; revised on February 22, 2001
; accepted on February 26, 2001
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% missing values. We show that KNNimpute appears to provide a more robust and sensitive method for missing value estimation than SVDimpute, and both SVDimpute and KNNimpute surpass the commonly used row average method (as well as filling missing values with zeros). We report results of the comparative experiments and provide recommendations and tools for accurate estimation of missing microarray data under a variety of conditions.
Availability: The software is available at http://smi-web.stanford.edu/projects/helix/pubs/impute/
Contact: russ.altman{at}stanford.edu
* To whom correspondence should be addressed.
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|
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|
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
Z. S. Qin Clustering microarray gene expression data using weighted Chinese restaurant process Bioinformatics, August 15, 2006; 22(16): 1988 - 1997. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
V. Dumeaux, J. Johansen, A.-L. Borresen-Dale, and E. Lund Gene expression profiling of whole-blood samples from women exposed to hormone replacement therapy. Mol. Cancer Ther., April 1, 2006; 5(4): 868 - 876. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Barutcuoglu, R. E. Schapire, and O. G. Troyanskaya Hierarchical multi-label prediction of gene function Bioinformatics, April 1, 2006; 22(7): 830 - 836. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Gan, A. W.-C. Liew, and H. Yan Microarray missing data imputation based on a set theoretic framework and biological knowledge Nucleic Acids Res., March 20, 2006; 34(5): 1608 - 1619. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Missal, M. A. Cross, and D. Drasdo Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment Bioinformatics, March 15, 2006; 22(6): 731 - 738. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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|
|
|
|
|
|
L. Li Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information Bioinformatics, February 15, 2006; 22(4): 466 - 471. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. T. Leek, E. Monsen, A. R. Dabney, and J. D. Storey EDGE: extraction and analysis of differential gene expression Bioinformatics, February 15, 2006; 22(4): 507 - 508. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
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|
|