Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data
1 Pulmonary Gene Research, University Hospital Basel, CH-4031 Basel, Switzerland
2 Laboratoire de Biométrie et de Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, 43 blvd du 11 Novembre, 1918, 69622 Villeurbanne Cedex, France
3 Bioinformatics Conway Institute, University College Dublin, Ireland
BMC Bioinformatics 2005, 6:239 doi:10.1186/1471-2105-6-239Published: 28 September 2005
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.
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.
OBC considerably improved the classification and predictive accuracy of BGA, when assessed using independent data sets and leave-one-out cross-validation.
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