simpler evaluation of predictions and signature stability for gene expression data简单的评估预测基因表达数据的稳定性和签名.pdfVIP

Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2009, Article ID 587405, 7 pages doi:10.1155/2009/587405 Research Article Simpler Evaluation of Predictions and Signature Stability for Gene Expression Data Yvonne E. Pittelkow1 and Susan R. Wilson1, 2 1 Centre for Bioinformation Science, MSI, The Australian National University, Canberra, ACT 0200, Australia 2 School of Mathematics Statistics, Faculty of Science, Prince of Wales Clinical School, Faculty of Medicine, University of NSW, Sydney 2052, Australia Correspondence should be addressed to Yvonne E. Pittelkow, yvonne.pittelkow@.au Received 3 March 2009; Revised 31 July 2009; Accepted 3 November 2009 Recommended by Satoru Miyano Scientific advances are raising expectations that patient-tailored treatment will soon be available. The development of resulting clinical approaches needs to be based on well-designed experimental and observational procedures that provide data to which proper biostatistical analyses are applied. Gene expression microarray and related technology are rapidly evolving. It is providing extremely large gene expression profiles containing many thousands of measurements. Choosing a subset from these gene expression measurements to include in a gene expression signature is one of the many challenges needing to be met. Choice of this signature depends on many factors, including the selection of patients in the training set. So the reliability and reproducibility of the resultant prognostic gene signature needs to be evaluated, in such a way as to be relevant to the clinical setting. A relatively straightforward approach is based on cross validation, with separate selection of genes at each iteration to avoid selection bias. Within this approach we developed