multtest: Resampling-based multiple hypothesis testing. Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

References in zbMATH (referenced in 22 articles )

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  1. Mair, Patrick: Modern psychometrics with R (2018)
  2. Kris Sankaran; Susan Holmes: structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data (2014) not zbMATH
  3. Lourenço, V. M.; Pires, A. M.: M-regression, false discovery rates and outlier detection with application to genetic association studies (2014)
  4. Miecznikowski, Jeffrey C.; Gaile, Daniel P.: A novel characterization of the generalized family wise error rate using empirical null distributions (2014)
  5. Vsevolozhskaya, Olga; Greenwood, Mark; Holodov, Dmitri: Pairwise comparison of treatment levels in functional analysis of variance with application to erythrocyte hemolysis (2014)
  6. Vsevolozhskaya, O. A.; Greenwood, M. C.; Bellante, G. J.; Powell, S. L.; Lawrence, R. L.; Repasky, K. S.: Combining functions and the closure principle for performing follow-up tests in functional analysis of variance (2013)
  7. Yata, Kazuyoshi; Aoshima, Makoto: Correlation tests for high-dimensional data using extended cross-data-matrix methodology (2013)
  8. Yata, Kazuyoshi; Aoshima, Makoto: Inference on high-dimensional mean vectors with fewer observations than the dimension (2012)
  9. Miecznikowski, Jeffrey C.; Gold, David; Shepherd, Lori; Liu, Song: Deriving and comparing the distribution for the number of false positives in single step methods to control (k)-FWER (2011)
  10. Stevens, John R.; Bell, Jason L.; Aston, Kenneth I.; White, Kenneth L.: A comparison of probe-level and probeset models for small-sample gene expression data (2010) ioport
  11. Yata, Kazuyoshi; Aoshima, Makoto: Intrinsic dimensionality estimation of high-dimension, low sample size data with (D)-asymptotics (2010)
  12. Causeur, D.; Kloareg, M.; Friguet, C.: Control of the FWER in multiple testing under dependence (2009)
  13. Hackstadt, Amber J.; Hess, Ann M.: Filtering for increased power for microarray data analysis (2009) ioport
  14. Tuglus, Catherine; Van der Laan, Mark J.: Modified FDR controlling procedure for multi-stage analyses (2009)
  15. Dudoit, Sandrine; Gilbert, Houston N.; van der Laan, Mark J.: Resampling-based empirical Bayes multiple testing procedures for controlling generalized tail probability and expected value error rates: focus on the false discovery rate and simulation study (2008)
  16. Dudoit, Sandrine; Keleş, Sündüz; van der Laan, Mark J.: Multiple tests of association with biological annotation metadata (2008)
  17. Shilane, David; Martikainen, Jarno; Dudoit, Sandrine; Ovaska, Seppo J.: A general framework for statistical performance comparison of evolutionary computation algorithms (2008) ioport
  18. Torsten Hothorn; Kurt Hornik; Mark van de Wiel; Achim Zeileis: Implementing a Class of Permutation Tests: The coin Package (2008) not zbMATH
  19. Juan R. González, Lluís Armengol, Xavier Solé, Elisabet Guinó, Josep M. Mercader, Xavier Estivill, Víctor Moreno : SNPassoc: an R package to perform whole genome association studies (2007) not zbMATH
  20. Segal, Mark R.: Validation in genomics: CPG island methylation revisited (2006)

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