Search PubMed⌕ Search

PubMed · 10544312

Asymptotic power calculations: description, examples, computer code.

Abstract

This paper describes two asymptotic methods for sample size and power calculation for hypothesis testing. Both methods assume that the distribution of the likelihood ratio is approximately distributed as a central chi(2) distribution under the null hypothesis and as a non-central chi(2) under the alternative hypothesis. The approximation to the non-centrality parameter differs between the methods. It is shown how these methods can be automatically extended from constraints setting parameters to constant values to constraints positing equality of parameters. Two very simple examples are presented; one demonstrates that the information method can produce arbitrarily incorrect results. Four more comprehensive examples are then discussed. In addition to demonstrating the wide range of applicability of these methods, the examples illustrate techniques that may be used in cases in which there is insufficient initial information available to perform a realistic calculation. The availability of a computer implementation of these methods in S-plus is announced, as are routines for computing the cumulative distribution function of the non-central chi(2) and its inverse.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

B W Brown, J Lovato, K Russell. 1999-11-30. Asymptotic power calculations: description, examples, computer code.. https://doi.org/10.1002/(sici)1097-0258(19991130)18%3A22%3C3137%3A%3Aaid-sim239%3E3.0.co%3B2-o

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

Generating correlated data for omics simulation.

Simulation of realistic omics data is a key input for benchmarking studies that help users obtain optimal computational pipelines. Omics data involves large numbers of measured features on each sample and these measures are generally correlated with each other. However, simulation too often ignores these correlations, perhaps due to computational and statistical hurdles of doing so. To alleviate this, we describe three approaches for generating omics-scale data with correlated measures which mimic real datasets. These approaches are all based on a Gaussian copula approach with a covariance matrix that decomposes into a diagonal part and a low-rank part. This decomposition allows for extremely efficient simulation, overcoming a hurdle for adoption of past methods. We use these approaches to demonstrate the importance of including correlation in two benchmarking applications. First, we show that variance of results from the popular DESeq2 method increases when dependence is included. Second, we demonstrate that CYCLOPS, a method for inferring circadian time of collection from transcriptomics, improves in performance when given gene-gene dependencies in some circumstances. We provide an R package, dependentsimr, that has efficient implementations of these methods and can generate dependent data with arbitrary marginal distributions, including discrete (binary, ordered categorical, Poisson, negative binomial), continuous (normal), or with an empirical distribution.

Computer Simulation↗

Addressing current challenges in cancer immunotherapy with mathematical and computational modelling.

The goal of cancer immunotherapy is to boost a patient's immune response to a tumour. Yet, the design of an effective immunotherapy is complicated by various factors, including a potentially immunosuppressive tumour microenvironment, immune-modulating effects of conventional treatments and therapy-related toxicities. These complexities can be incorporated into mathematical and computational models of cancer immunotherapy that can then be used to aid in rational therapy design. In this review, we survey modelling approaches under the umbrella of the major challenges facing immunotherapy development, which encompass tumour classification, optimal treatment scheduling and combination therapy design. Although overlapping, each challenge has presented unique opportunities for modellers to make contributions using analytical and numerical analysis of model outcomes, as well as optimization algorithms. We discuss several examples of models that have grown in complexity as more biological information has become available, showcasing how model development is a dynamic process interlinked with the rapid advances in tumour-immune biology. We conclude the review with recommendations for modellers both with respect to methodology and biological direction that might help keep modellers at the forefront of cancer immunotherapy development.

Computer Simulation↗

Oligonucleotide mapping of the core genomic RNA dimer linkage in human T-cell leukaemia virus type-1.

We have previously mapped the sequences required for dimerisation of the 5' leader of the human T-cell leukaemia virus type-1 (HTLV-1) genome. The smallest sequence necessary and sufficient for dimer formation, in vitro, was ascertained to be a 37 nucleotide (nt) region downstream of the splice donor and just upstream of the primer binding site. Deletion of a 32 base-pair sequence encompassing this region within the provirus was associated with a minor decrease in infectivity of the virus in an in vitro system. To further map and help elucidate the nature of the dimer linkage, we used RNA and DNA oligonucleotide competition assays to define the nucleotides involved. These experiments revealed that a 14 nt sequence containing a potential stem loop structure, formed from a palindromic sequence, is important for dimer formation. This was confirmed by the ability of this RNA sequence to form heterodimers with larger RNA transcripts from the same region, while sequences lacking this motif could not. RNA transcripts containing the reverse sequence, the same nucleotides in a random arrangement, and complementary DNA oligos, all failed to form heterodimers with the 14 nt sequence. The primary dimer initiation site of HTLV-1 has thus been located to a 14 nt palindrome containing sequence, and dimerisation is shown to be dependent on specific sense-sense RNA interactions.

Computer Simulation↗