Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data

Abstract

Abstract Background A recent publication described a supervised classification method for microarray data: Between Group Analysis (BGA). This method which is based on performing multivariate ordination of groups proved to be very efficient for both classification of samples into pre-defined groups and disease class prediction of new unknown samples. Classification and prediction with BGA are classically performed using the whole set of genes and no variable selection is required. We hypothesize that an optimized selection of highly discriminating genes might improve the prediction power of BGA. Results We propose an optimized between-group classification (OBC) which uses a jackknife-based gene selection procedure. OBC emphasizes classification accuracy rather than feature selection. OBC is a backward optimization procedure that maximizes the percentage of between group inertia by removing the least influential genes one by one from the analysis. This selects a subset of highly discriminative genes which optimize disease class prediction. We apply OBC to four datasets and compared it to other classification methods. Conclusion OBC considerably improved the classification and predictive accuracy of BGA, when assessed using independent data sets and leave-one-out cross-validation. Availability The R code is freely available [see Additional file 1] as well as supplementary information [see Additional file 2]. Additional File 1 R code of the OBC algorithm. Click here for file Additional File 2 Further description of the sarcoidosis and tumour data. This files gives details about the optimal subset of genes obtained after OBC. Click here for file