Classification Accuracy Based Microarray Missing Value Imputation

Bioinformatics Algorithms: Techniques and Applications

Volumn , Issue , 2007, Pages 303-327

  Shi, Yi ^a   Cai, Zhipeng ^a   Lin, Guohui ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Affymetrix GeneChip oligonucleotide (Affy) arrays; Gene expression microarray; Singular Value Decomposition (SVDimpute)

Indexed keywords

EID: 43849089338     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470253441.ch14     Document Type: Chapter

References (20)

1. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson Jr J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, and Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-511.
2. Baldi P, Long AD. A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 2001;17: 509-519.
3. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerso M. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Nat Acad Sci USA 2001;98:13790-13795.
4. Bø TH, Dysvik B, Jonassen I. LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucl Acid Res 2004;32:e34.
5. Cai Z, Heydari M, Lin G-H. Iterated local least squares microarray missing value imputation. J Bioinformatics Comput Biol 2006;4(5):935-957.
6. Dudoit S, Fridlyand J, Speed TP. Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc 2002;97:77-87.
7. Guyon I, Weston J, Barnhill S, Vapnik V. Gene selection for cancer classification using support vector machines. Mach Learn 2002;46:389-422.
8. Jörnsten R, Wang H-Y, Welsh WJ, Ouyang M. DNA microarray data imputation and significance analysis of differential expression. Bioinformatics 2005;21:4155-4161.
9. Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, Meltzer PS. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001;7:673-679.
10. Kim H, Golub GH, Park H. Missing value estimation for DNA microarray gene expression data: Local least squares imputation. Bioinformatics 2005;21:187-198.
11. Kim K-Y, Kim B-J, Yi G-S. Reuse of imputed data in microarray analysis increases imputation efficiency. BMC Bioinformatics 2004;5:160
12. Nutt CL, Mani DR, Betensky RA, Tamayo P, Cairncross JG, Ladd C, Pohl U, Hartmann C, McLaughlin ME, Batchelor TT, Black PM, Deimling AV, Pomeroy SL, Golub TR, Louis DN. Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res 2003;63:1602-1607.
13. Oba S, Sato M, Takemasa I, Monden M, Matsubara K, Ishii S. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 2003;19:2088-2096.
14. Ouyang M, Welsh WJ, Georgopoulos P. Gaussian mixture clustering and imputation of microarray data. Bioinformatics 2004;20:917-923.
15. Scheel I, Aldrin M, Glad IK, Sørum R, Lyng H, Frigessi A. The influence of missing value imputation on detection of differentially expressed genes from microarray data. Bioinformatics 2005;21:4272-4279.
16. Sehgal MSB, Gondal L, Dooley LS. Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data. Bioinformatics 2005;21:2417-2423.
17. Suárez-Fariñas M, Haider A, Wittkowski KM. "Harshlighting" small blemishes on microarrays. BMC Bioinformatics 2005;6:65
18. Troyanskaya OG, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays. Bioinformatics 2001;17:520-525.
19. Xiong M, Fang X, Zhao J. Biomarker identification by feature wrappers. Genome Res 2001;11:1878-1887.
20. Yang K, Cai Z, Li J, Lin G-H. A stable gene selection in microarray data analysis. BMC Bioinformatics 2006;7:228