Factor analysis for cross-platform tumor classification based on gene expression profiles

Previous studies on tumor classification based on feature extraction from gene expression profiles (GEP) were proven to be effective, but some of such methods lack biomedical meaning to some extent. To deal with this problem, we proposed a novel feature extraction method whose experimental results are of biomedical interpretability and helpful for gaining insight into the structure analysis of gene expression dataset. This method first applied rank sum test to roughly select a set of informative genes and then adopted factor analysis to extract latent factors for tumor classification. Experiments on three pairs of cross-platform tumor datasets indicated that the proposed method can obviously improve the performance of cross-platform classification and only several latent factors, which can represent a large number of informative genes, would obtain very high predictive accuracy on test set. The results also suggested that the classification model trained on one dataset can successfully predict another tumor dataset with the same tumor subtype obtained on different experimental platforms.