Iterative bicluster-based least square framework for estimation of missing values in microarray gene expression data

Authors:
K. O. Cheng;N. F. Law;W. C. Siu
Affiliations:
Center for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong;Center for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong;Center for Signal Processing, Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
Venue:
Pattern Recognition
Year:
2012

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Abstract

DNA microarray experiment inevitably generates gene expression data with missing values. An important and necessary pre-processing step is thus to impute these missing values. Existing imputation methods exploit gene correlation among all experimental conditions for estimating the missing values. However, related genes coexpress in subsets of experimental conditions only. In this paper, we propose to use biclusters, which contain similar genes under subset of conditions for characterizing the gene similarity and then estimating the missing values. To further improve the accuracy in missing value estimation, an iterative framework is developed with a stopping criterion on minimizing uncertainty. Extensive experiments have been conducted on artificial datasets, real microarray datasets as well as one non-microarray dataset. Our proposed biclusters-based approach is able to reduce errors in missing value estimation.