A hybrid imputation approach for microarray missing value estimation

BMC Genomics
Huihui LiXiao Wang

Abstract

Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used methods for processing missing data. Actually many developments have been achieved in the research on estimating missing values. The challenging task is how to improve imputation accuracy for data with a large missing rate. In this paper, induced by the thought of collaborative training, we propose a novel hybrid imputation method, called Recursive Mutual Imputation (RMI). Specifically, RMI exploits global correlation information and local structure in the data, captured by two popular methods, Bayesian Principal Component Analysis (BPCA) and Local Least Squares (LLS), respectively. Mutual strategy is implemented by sharing the estimated data sequences at each recursive process. Meanwhile, we consider the imputation sequence based on the number of missing entries in the target gene. Furthermore, a weight based integrated method is utilized in the final assembling step. We evaluate RMI with three state-of-art algorithms (BPCA, LLS...Continue Reading

References

Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·O AlterD Botstein
Jun 8, 2001·Bioinformatics·O TroyanskayaR B Altman
Aug 2, 2001·Biochemical and Biophysical Research Communications·I TakemasaK Matsubara
Nov 5, 2003·Bioinformatics·Shigeyuki ObaShin Ishii
Aug 25, 2005·Bioinformatics·Rebecka JörnstenMing Ouyang
Dec 31, 2005·Proceedings of the National Academy of Sciences of the United States of America·Michal Ronen, David Botstein
Nov 14, 2006·Journal of Bioinformatics and Computational Biology·Zhipeng CaiGuohui Lin
Oct 3, 2008·Computers in Biology and Medicine·Xiaobai ZhangHuanping Zhang
Aug 5, 2010·International Journal of Data Mining and Bioinformatics·Wai-Ki ChingKwai-Wa Cheng
Oct 18, 2013·IEEE Journal of Biomedical and Health Informatics·Fanchi MengHong Yan

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Citations

Jan 24, 2017·IEEE Transactions on Nanobioscience·Zeng YuYunge Jing

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Methods Mentioned

BETA
PCA

Software Mentioned

Tacrc
ItrLLS
EMDI
Elu
Ronen
LinCmb
Alpha
LLS
COREG
RMI

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