6,909 research outputs found
Faster Family-wise Error Control for Neuroimaging with a Parametric Bootstrap
In neuroimaging, hundreds to hundreds of thousands of tests are performed
across a set of brain regions or all locations in an image. Recent studies have
shown that the most common family-wise error (FWE) controlling procedures in
imaging, which rely on classical mathematical inequalities or Gaussian random
field theory, yield FWE rates that are far from the nominal level. Depending on
the approach used, the FWER can be exceedingly small or grossly inflated. Given
the widespread use of neuroimaging as a tool for understanding neurological and
psychiatric disorders, it is imperative that reliable multiple testing
procedures are available. To our knowledge, only permutation joint testing
procedures have been shown to reliably control the FWER at the nominal level.
However, these procedures are computationally intensive due to the increasingly
available large sample sizes and dimensionality of the images, and analyses can
take days to complete. Here, we develop a parametric bootstrap joint testing
procedure. The parametric bootstrap procedure works directly with the test
statistics, which leads to much faster estimation of adjusted \emph{p}-values
than resampling-based procedures while reliably controlling the FWER in sample
sizes available in many neuroimaging studies. We demonstrate that the procedure
controls the FWER in finite samples using simulations, and present region- and
voxel-wise analyses to test for sex differences in developmental trajectories
of cerebral blood flow
A statistical framework for testing functional categories in microarray data
Ready access to emerging databases of gene annotation and functional pathways
has shifted assessments of differential expression in DNA microarray studies
from single genes to groups of genes with shared biological function. This
paper takes a critical look at existing methods for assessing the differential
expression of a group of genes (functional category), and provides some
suggestions for improved performance. We begin by presenting a general
framework, in which the set of genes in a functional category is compared to
the complementary set of genes on the array. The framework includes tests for
overrepresentation of a category within a list of significant genes, and
methods that consider continuous measures of differential expression. Existing
tests are divided into two classes. Class 1 tests assume gene-specific measures
of differential expression are independent, despite overwhelming evidence of
positive correlation. Analytic and simulated results are presented that
demonstrate Class 1 tests are strongly anti-conservative in practice. Class 2
tests account for gene correlation, typically through array permutation that by
construction has proper Type I error control for the induced null. However,
both Class 1 and Class 2 tests use a null hypothesis that all genes have the
same degree of differential expression. We introduce a more sensible and
general (Class 3) null under which the profile of differential expression is
the same within the category and complement. Under this broader null, Class 2
tests are shown to be conservative. We propose standard bootstrap methods for
testing against the Class 3 null and demonstrate they provide valid Type I
error control and more power than array permutation in simulated datasets and
real microarray experiments.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS146 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Accelerating Permutation Testing in Voxel-wise Analysis through Subspace Tracking: A new plugin for SnPM
Permutation testing is a non-parametric method for obtaining the max null
distribution used to compute corrected -values that provide strong control
of false positives. In neuroimaging, however, the computational burden of
running such an algorithm can be significant. We find that by viewing the
permutation testing procedure as the construction of a very large permutation
testing matrix, , one can exploit structural properties derived from the
data and the test statistics to reduce the runtime under certain conditions. In
particular, we see that is low-rank plus a low-variance residual. This
makes a good candidate for low-rank matrix completion, where only a very
small number of entries of ( of all entries in our experiments)
have to be computed to obtain a good estimate. Based on this observation, we
present RapidPT, an algorithm that efficiently recovers the max null
distribution commonly obtained through regular permutation testing in
voxel-wise analysis. We present an extensive validation on a synthetic dataset
and four varying sized datasets against two baselines: Statistical
NonParametric Mapping (SnPM13) and a standard permutation testing
implementation (referred as NaivePT). We find that RapidPT achieves its best
runtime performance on medium sized datasets (), with
speedups of 1.5x - 38x (vs. SnPM13) and 20x-1000x (vs. NaivePT). For larger
datasets () RapidPT outperforms NaivePT (6x - 200x) on all
datasets, and provides large speedups over SnPM13 when more than 10000
permutations (2x - 15x) are needed. The implementation is a standalone toolbox
and also integrated within SnPM13, able to leverage multi-core architectures
when available.Comment: 36 pages, 16 figure
Exact and Asymptotic Weighted Logrank Tests for Interval Censored Data: The interval R Package
For right-censored data perhaps the most commonly used tests are weighted logrank tests, such as the logrank and Wilcoxon-type tests. In this paper we review several generalizations of those weighted logrank tests to interval-censored data and present an R package, interval, to implement many of them. The interval package depends on the perm package, also presented here, which performs exact and asymptotic linear permutation tests. The perm package performs many of the tests included in the already available coin package, and provides an independent validation of coin. We review analysis methods for interval-censored data, and we describe and show how to use the interval and perm packages.
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