Relation Between Permutation-Test P Values and Classifier Error Estimates (original) (raw)
References
Allander, S. V., Nupponen, N. N., Ringner, M., Hostetter, G., Maher, Goldberger, N., Chen, Y., Carpten, J., Elkahloun, A. G., & Meltzer, P. S. (2001). Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile. Cancer Research, 61, 8624–8628. Google Scholar
Armstrong, S. A. et al. (2002). MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nature Genetics, 30, 41–47. Google Scholar
Ben-Dor, A., Bruhn, L., Friedman, N., Nachman, I., Schummer, M., & Yakhini, Z. (2000). Tissue classification with gene expression profiles. Computational Biology, 7, 559–583. Google Scholar
Bhattacharjee, A. et al. (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proceedings of the National Academy of Sciences, 98:24, 13790–13795 Google Scholar
De Risi, J. L., Iyer, V. R., & Brown, P. O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680–686. Google Scholar
Devroye, L., Gyorfi, L., & Lugosi, G. (1996). _A Probabilistic Theory of Pattern Recognitio_n. New York: Springer-Verlag. Google Scholar
Dougherty, E. R. (2001). Small sample issues for microarray-based classification. Comparative and Functional Genomics, 2, 28–34. Google Scholar
Duggan, D. J., Bittner, M. L., Chen, Y., Meltzer, P. S., & Trent, J. M. (1999). Expression profiling using cDNA microarrays. Nature Genetics, 21, 10–14. Google Scholar
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., & Lander, E. S. (1999). Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science, 286, 531–537. Google Scholar
Good, P. (1994). _Permutation Tests: A Practical Guide to Resampling Methods for Testing Hypothesi_s. New York: Springer-Verlag. Google Scholar
Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Raffeld, Yakhini, Z., Ben-Dor, A., Dougherty, E., Kononen, J., Bubendorf, L., Fehrle, W., Pittaluga, S., Gruvverger, S., Loman, N., Johannsson, O., Olsson, H., Wifond, B., Sauter, G., Kallioniemi, O. P., Borg, A., & Trent, J. (2001). Gene expression profiles distinguish hereditary breast cancers. New England Journal of Medicine, 34, 539–548. Google Scholar
Khan, J., Wei, J. S., Ringner, M., Saal, L. H., Ladanyi, M., Westermann, F., Berthold, F., Schwab, M., Antonescu, C. R., Peterson, C., & Meltzer, P. S. (2001). Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Natture Medicine, 7, 673–679. Google Scholar
Lesnick, S. T., Dacwag, C. S., & Golub, T. R. (2002). The Ewing's sarcoma oncoprotein EWS/FLI induces p 53-dependent growth arrest in primary human fibroblasts. Cancer Cell, 1, 393–401. Google Scholar
Pomeroy, S. L., Tamayo, P., Gaasenbeek, M., Sturla, L. M., Angelo, M., McLaughlin, Kim, J. Y. H., Goumnerova,. C., Black, P., Lau, C., Allen, J. C., Zagzag, D., Olson, J. M., Curran, T., Wetmore, C., Biegel, J. A., Poggio, T., Mukherjee, C., Rifkin, R., Califano, A., Stolovitzky, G., Louis, D. N., Mesirov, J. P., Lander, E. S., & Golub, T. R. (2002). Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature, 415, 436–442. Google Scholar
Ramaswamy, S. et al. (2001). Multi-class cancer diagnosis using tumor gene expression signatures. Proceedings of the National Academy of Sciences, 98, 15149–15154. Google Scholar
Rogers, W., & Wagner, T. (1978). A finite sample distribution-free performance bound for local discrimination rules. Annals of Statistics, 8, 506–514. Google Scholar
Schena, M., Shalon, D., Davis, R. W., & Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467–470. Google Scholar
Slonim, D. K., Tamayo, P., Mesirov, J. P., Golub, T. R., & Lander, E. S. (2000). Class prediction and discovery using gene expression aata. _Annual Conference on Research in Computational Molecular Biolog_y, Tokyo.
Vapnik, V., & Chervonenkis, A. (1971). On the uniform convergence of relative frequencies of events to their probabilities. Theory of Probability and its Applications, 16, 264–280. Google Scholar
Yeang, C.-H. et al. (2001). Molecular classification of multiple tumor types. Bioinformatics. 17(Supplement 1): S316–S322. Google Scholar