A hybrid of SVM and SCAD with group-specific tuning parameter for pathway-based microarray analysis

Abstract

The incorporation of pathway data into the microarray analysis had lead to a new era in advance understanding of biological processes. However, this advancement is limited by the two issues in quality of pathway data. First, the pathway data are usually made from the biological context free, when it comes to a specific cellular process (e.g. lung cancer development), it can be that only several genes within pathways are responsible for the corresponding cellular process. Second, pathway data commonly curated from the literatures, it can be that some pathway may be included with the uninformative genes while the informative genes may be excluded. In this paper, we proposed a hybrid of support vector machine and smoothly clipped absolute deviation with group-specific tuning parameters (gSVM-SCAD) to select informative genes within pathways before the pathway evaluation process. Our experiments on lung cancer and gender data sets show that gSVM-SCAD obtains significant results in classification accuracy and in selecting the informative genes and pathways.