Biomarker discovery: classification using pooled samples

Abstract

RNA-sample pooling is sometimes inevitable, but should be avoided in classification tasks like biomarker studies. Our simulation framework investigates a two-class classification study based on gene expression profiles to point out how strong the outcomes of single sample designs differ to those of pooling designs. The results show how the effects of pooling depend on pool size, discriminating pattern, number of informative features and the statistical learning method used (support vector machines with linear and radial kernel, random forest (RF), linear discriminant analysis, powered partial least squares discriminant analysis (PPLS-DA) and partial least squares discriminant analysis (PLS-DA)). As a measure for the pooling effect, we consider prediction error (PE) and the coincidence of important feature sets for classification based on PLS-DA, PPLS-DA and RF. In general, PPLS-DA and PLS-DA show constant PE with increasing pool size and low PE for patterns for which the convex hull of one class is not a cover of the other class. The coincidence of important feature sets is larger for PLS-DA and PPLS-DA as it is for RF. RF shows the best results for patterns in which the convex hull of one class is a cover of the other class, but these depend strongly on the pool size. We complete the PE results with experimental data which we pool artificially. The PE of PPLS-DA and PLS-DA are again least influenced by pooling and are low. Additionally, we show under which assumption the PLS-DA loading weights, as a measure for importance of features regarding classification, are equal for the different designs.