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 12 articles )

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  1. Kris Sankaran; Susan Holmes: structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data (2014)
  2. Vsevolozhskaya, Olga; Greenwood, Mark; Holodov, Dmitri: Pairwise comparison of treatment levels in functional analysis of variance with application to erythrocyte hemolysis (2014)
  3. Yata, Kazuyoshi; Aoshima, Makoto: Correlation tests for high-dimensional data using extended cross-data-matrix methodology (2013)
  4. Yata, Kazuyoshi; Aoshima, Makoto: Inference on high-dimensional mean vectors with fewer observations than the dimension (2012)
  5. 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)
  6. Yata, Kazuyoshi; Aoshima, Makoto: Intrinsic dimensionality estimation of high-dimension, low sample size data with $D$-asymptotics (2010)
  7. Causeur, D.; Kloareg, M.; Friguet, C.: Control of the FWER in multiple testing under dependence (2009)
  8. Tuglus, Catherine; Van der Laan, Mark J.: Modified FDR controlling procedure for multi-stage analyses (2009)
  9. Dudoit, Sandrine; Keleş, Sündüz; van der Laan, Mark J.: Multiple tests of association with biological annotation metadata (2008)
  10. Torsten Hothorn; Kurt Hornik; Mark van de Wiel; Achim Zeileis: Implementing a Class of Permutation Tests: The coin Package (2008)
  11. Segal, Mark R.: Validation in genomics: CPG island methylation revisited (2006)
  12. Gentleman, Robert (ed.); Carey, Vincent J. (ed.); Huber, Wolfgang (ed.); Irizarry, Rafael A. (ed.); Dudoit, Sandrine (ed.): Bioinformatics and computational biology solutions using R and Bioconductor. (2005)