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This paper proposes a new missing value imputation method for microarray data using ensemble technique (KNN-Ensemble). We run an experiment on three standard benchmark microarray datasets: Colon, Prostate and Ovarian. Four different distance functions for KNN imputation method were studied. Our experiment can be separated into three steps: (1) selecting two best distance functions for KNN imputation; one distance function for evaluating sample distance and another one is the best distance function used to evaluate distance between features (2) estimating missing values using KNN-Ensemble based on two selected functions
from the first step and (3) evaluating the performance of new imputation method for microarray data using ensemble approach with other well-known imputation algorithms: original KNN and Row-Average imputation. The experimental results show that KNN-Ensemble method using Manhattan and Euclidian distance function outperformed other baseline imputation methods on three datasets.