Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments.

BMC Genomics ISI Document Delivery No.: 565GZ Times Cited: 11 Cited Reference Count: 84 Celton, Magalie Malpertuy, Alain Lelandais, Gaelle de Brevern, Alexandre G. Ministere de la Recherche; French Institute for Health and Medical Research (INSERM); Universite - Paris Diderot Paris 7; Institut National de Transfusion Sanguine (INTS) and Genopole(R); Clustering Agreement Ration (CAR) We would like to thanks all the scientists who have deposited their experiments and make them freely available to the scientific community. In the same way, we would like to thanks all the scientists who have developed and distributed missing value replacement methods. This work was supported by grants from the Ministere de la Recherche, from French Institute for Health and Medical Research (INSERM), Universite - Paris Diderot Paris 7, Institut National de Transfusion Sanguine (INTS) and Genopole (R). Clustering Agreement Ration (CAR) was proposed by late Pr. Serge Hazout. Biomed central ltd LondonInternational audienceBACKGROUND: Microarray technologies produced large amount of data. In a previous study, we have shown the interest of k-Nearest Neighbour approach for restoring the missing gene expression values, and its positive impact of the gene clustering by hierarchical algorithm. Since, numerous replacement methods have been proposed to impute missing values (MVs) for microarray data. In this study, we have evaluated twelve different usable methods, and their influence on the quality of gene clustering. Interestingly we have used several datasets, both kinetic and non kinetic experiments from yeast and human. RESULTS: We underline the excellent efficiency of approaches proposed and implemented by Bo and co-workers and especially one based on expected maximization (EM_array). These improvements have been observed also on the imputation of extreme values, the most difficult predictable values. We showed that the imputed MVs have still important effects on the stability of the gene clusters. The improvement on the clustering obtained by hierarchical clustering remains limited and, not sufficient to restore completely the correct gene associations. However, a common tendency can be found between the quality of the imputation method and the gene cluster stability. Even if the comparison between clustering algorithms is a complex task, we observed that k-means approach is more efficient to conserve gene associations. CONCLUSIONS: More than 6.000.000 independent simulations have assessed the quality of 12 imputation methods on five very different biological datasets. Important improvements have so been done since our last study. The EM_array approach constitutes one efficient method for restoring the missing expression gene values, with a lower estimation error level. Nonetheless, the presence of MVs even at a low rate is a major factor of gene cluster instability. Our study highlights the need for a systematic assessment of imputation methods and so of dedicated benchmarks. A noticeable point is the specific influence of some biological dataset