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RDCurve: A Nonparametric Method to Evaluate the Stability of Ranking Procedures
PrePrint
ISSN: 1545-5963
Xin Lu, University of California, San Diego, CA
Anthony Gamst, University of California, San Diego, CA
Ronghui Xu, University of California, San Diego, CA
Great concerns have been raised about the reproducibility of gene signatures based on high-throughput techniques such as microarray. Studies analyzing similar samples often report poorly overlapping results, and the p-value usually lacks biological context. We propose a non-parametric Re-Discovery-Curve (RDCurve) method, to estimate the frequency of rediscovery of gene signature identified. Given a ranking procedure and a dataset with replicated measurements, the RDCurve bootstraps the dataset and repeatedly applies the ranking procedure, selects a subset of k important genes, and estimates the probability of rediscovery of the selected subset of genes. We also propose a permutation scheme to estimate the confidence band under the Null hypothesis for the significance of the RDCurve. The method is non-parametric and model independent. With the RDCurve we can assess the signal-noise ratio of the data, compare the performance of ranking procedures in term of their expected rediscovery rates, and choose the number of genes to be reported.
Index Terms:
Biology and genetics, Life and Medical Sciences, Computer Applications, Multivariate statistics, Nonparametric statistics
Citation:
Xin Lu, Anthony Gamst, Ronghui Xu, "RDCurve: A Nonparametric Method to Evaluate the Stability of Ranking Procedures," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19 Dec. 2008. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.138>
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