Classification based on extensions of LS-PLS using logistic regression: Application to clinical and multiple genomic data

Abstract

Background: To address high-dimensional genomic data, most of the proposed prediction methods make use of genomic data alone without considering clinical data, which are often available and known to have predictive value. Recent studies suggest that combining clinical and genomic information may improve predictions. We consider here methods for classification purposes that simultaneously use both types of variables but apply dimensionality reduction only to the high-dimensional genomic ones. Results: Using partial least squares (PLS), we propose some one-step approaches based on three extensions of the least squares (LS)-PLS method for logistic regression. A comparison of their prediction performances via a simulation and on real data sets from cancer studies is conducted. Conclusion: In general, those methods using only clinical data or only genomic data perform poorly. The advantage of using LS-PLS methods for classification and their performances are shown and then used to analyze clinical and genomic data. The corresponding prediction results are encouraging and stable regardless of the data set and/or number of selected features. These extensions have been implemented in the R package lsplsGlm to enhance their use.