Background: The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context.

Abstract-We present a novel framework that applies a metalearning approach to clustering algorithms. Given a dataset, our meta-learning approach provides a ranking for the candidate algorithms that could be used with that dataset. This ranking could, among other things, support non-expert users in the algorithm selection task. In order to evaluate the framework proposed, we implement a prototype that employs regression support vector machines as the meta-learner. Our case study is developed in the context of cancer gene expression microarray datasets.

Characteristics extracted from the training datasets of classification problems have proven to be effective predictors in a number of meta-analyses. Among them, measures of classification complexity can be used to estimate the difficulty in separating the data points into their expected classes. Descriptors of the spatial distribution of the data and estimates of the shape and size of the decision boundary are among the known measures for this characterization. This information can support the formulation of new data-driven pre-processing and pattern recognition techniques, which can in turn be focused on challenges highlighted by such characteristics of the problems. This article surveys and analyzes measures that can be extracted from the training datasets to characterize the complexity of the respective classification problems. Their use in recent literature is also reviewed and discussed, allowing to prospect opportunities for future work in the area. Finally, descriptions are given on an R package named Extended Complexity Library (ECoL) that implements a set of complexity measures and is made publicly available.

BackgroundSeveral missing value imputation methods for gene expression data have been proposed in the literature. In the past few years, researchers have been putting a great deal of effort into presenting systematic evaluations of the different imputation algorithms. Initially, most algorithms were assessed with an emphasis on the accuracy of the imputation, using metrics such as the root mean squared error. However, it has become clear that the success of the estimation of the expression value should be evaluated in more practical terms as well. One can consider, for example, the ability of the method to preserve the significant genes in the dataset, or its discriminative/predictive power for classification/clustering purposes.Results and conclusionsWe performed a broad analysis of the impact of five well-known missing value imputation methods on three clustering and four classification methods, in the context of 12 cancer gene expression datasets. We employed a statistical framework, for the first time in this field, to assess whether different imputation methods improve the performance of the clustering/classification methods. Our results suggest that the imputation methods evaluated have a minor impact on the classification and downstream clustering analyses. Simple methods such as replacing the missing values by mean or the median values performed as well as more complex strategies. The datasets analyzed in this study are available at http://costalab.org/Imputation/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0494-3) contains supplementary material, which is available to authorized users.