Mon Jun 29 08:21:42 2009; Christian Pipper

Mon Aug 31 14:05:45 2009; Christian Pipper

Tue Oct 20 09:07:48 2009; Christian Pipper

Christian B. Pipper <pipper@life.ku.dk>, Christian Ritz
<ritz@life.ku.dk>, Signe M. Jensen <smj@life.ku.dk>
R (>= 2.6.0), gtools, mvtnorm, sandwich, MASS, Rcpp

Christian B. Pipper <pipper@sund.ku.dk>, Christian Ritz
<ritz@life.ku.dk>, Signe M. Jensen <smj@life.ku.dk>

Katherine S. Pollard, Yongchao Ge, Sandra Taylor, Sandrine Dudoit
Non-parametric bootstrap and permutation resampling-based
multiple testing procedures 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). Single-step and step-wise
methods are implemented. Tests based on a variety of t- and
F-statistics (including t-statistics based on regression
parameters from linear and survival models) are included.
Results are reported in terms of adjusted p-values,
confindence regions and test statistic cutoffs. The procedures
are directly applicable to identifying differentially
expressed genes in DNA microarray experiments.
R (>= 2.1.0), methods, Biobase, survival

Katherine S. Pollard, Yongchao Ge, Sandrine Dudoit
Non-parametric bootstrap and permutation resampling-based multiple testing procedures 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). Single-step and step-wise methods are implemented. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models) are included. Results are reported in terms of adjusted p-values, confindence regions and test statistic cutoffs.

Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra
Taylor, Sandrine Dudoit
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.