Statistical test for ΔρDCCA : Methods and data.
Ontology highlight
ABSTRACT:
SUBMITTER: Guedes EF
PROVIDER: S-EPMC6103976 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:In educational measurement, exploring the method of generating multiple high-quality parallel tests has become a research hotspot. One purpose of this research is to construct parallel forms item by item according to a seed test, using two proposed item selection heuristic methods [minimum parameters-information-distance method (MPID) and minimum information-parameters-distance method (MIPD)]. Moreover, previous research addressing test assembly issues has been limited mainly to situations in which the information curve of the item pool or seed test has a normal or skewed distribution. However, in practice, the distributions of information curves for tests are diverse. These include multimodal distributions, the most common type of which is the bimodal distribution. Therefore, another main aim of this article is to extend the information curves of unimodal distributions to bimodal distributions. Thus, this study adopts simulation research to compare the results of two item, response, theory (IRT)-based item matching methods (MPID and MIPD) using different information curve distributions for item pools or seed tests. The results show that the MPID and MIPD methods yield rather good performance in terms of both two statistical targets when the information curve has a unimodal distribution, and two new methods yield better performance than two existing methods in terms of test information functions target when the information curve has a bimodal distribution.
| S-EPMC8873185 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2011-08-10 | GSE26736 | GEO
Project description:Background Many microarray experiments search for genes with differential expression between a common “reference” group and multiple test groups, like in the case of time-course designs or of various treatments versus a control condition. In such cases, currently employed statistical approaches based on t-test or close derivatives have limited efficacy, mostly because estimation of noise is done on only two groups at time. Alternative approaches based on ANOVA correctly capture noise from all the groups, but then do not confront single test groups with the reference. We therefore conceived a statistical test for pairwise comparisons between the reference group and each test group that uses within-group variance calculated from all the groups. Results We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s test, designed to compare multiple experimental groups against a common reference. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Thanks to automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied on a time-course experiment profiled in parallel on two microarray platforms, and compared with currently used tests, Mulcom displayed higher concordance of significant genes in the two array platforms, and higher enrichment in functional annotation to categories related to the biology of the experiment. Conclusions The Mulcom package provides a fast and powerful tool for the identification of differentially expressed genes when several experimental conditions are compared with a common reference. We found that Mulcom leads to lists of differentially expressed genes that are particularly consistent across microarray platforms and enriched in significant classes of genes. In our opinion, the main reasons for these good performances are three: (i) within-group variability is estimated from all experimental groups even if only two of them are compared each time; (ii) the optional fold-change threshold m avoids false positives due to aberrantly low within-group variability; (iii) automated test optimization allows maximizing sensitivity without compromising specificity.
2011-08-10 | GSE26735 | GEO
Project description:Background Many microarray experiments search for genes with differential expression between a common “reference” group and multiple test groups, like in the case of time-course designs or of various treatments versus a control condition. In such cases, currently employed statistical approaches based on t-test or close derivatives have limited efficacy, mostly because estimation of noise is done on only two groups at time. Alternative approaches based on ANOVA correctly capture noise from all the groups, but then do not confront single test groups with the reference. We therefore conceived a statistical test for pairwise comparisons between the reference group and each test group that uses within-group variance calculated from all the groups. Results We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s test, designed to compare multiple experimental groups against a common reference. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Thanks to automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied on a time-course experiment profiled in parallel on two microarray platforms, and compared with currently used tests, Mulcom displayed higher concordance of significant genes in the two array platforms, and higher enrichment in functional annotation to categories related to the biology of the experiment. Conclusions The Mulcom package provides a fast and powerful tool for the identification of differentially expressed genes when several experimental conditions are compared with a common reference. We found that Mulcom leads to lists of differentially expressed genes that are particularly consistent across microarray platforms and enriched in significant classes of genes. In our opinion, the main reasons for these good performances are three: (i) within-group variability is estimated from all experimental groups even if only two of them are compared each time; (ii) the optional fold-change threshold m avoids false positives due to aberrantly low within-group variability; (iii) automated test optimization allows maximizing sensitivity without compromising specificity.
2011-08-10 | GSE26732 | GEO
Project description:Big data are data on a massive scale in terms of volume, intensity, and complexity that exceed the capacity of standard analytic tools. They present opportunities as well as challenges to statisticians. The role of computational statisticians in scientific discovery from big data analyses has been under-recognized even by peer statisticians. This article summarizes recent methodological and software developments in statistics that address the big data challenges. Methodologies are grouped into three classes: subsampling-based, divide and conquer, and online updating for stream data. As a new contribution, the online updating approach is extended to variable selection with commonly used criteria, and their performances are assessed in a simulation study with stream data. Software packages are summarized with focuses on the open source R and R packages, covering recent tools that help break the barriers of computer memory and computing power. Some of the tools are illustrated in a case study with a logistic regression for the chance of airline delay.
| S-EPMC5041595 | biostudies-literature
Project description:As tools for quantitative label-free mass spectrometry (MS) rapidly develop a consensus about the best practices is not apparent. In the work described here we compared five popular statistical methods for detecting differential protein expression from quantitative MS data using both controlled experiments with known quantitative differences for specific proteins used as standards, as well as ‘real’ experiments where differences in protein abundance are not known a priori. Our results suggest that data-driven reproducibility-optimization can consistently produce reliable differential expression rankings for label-free proteome tools and are straightforward in their application.
2020-01-13 | PXD002099 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE26732: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor (Affymetrix) GSE26735: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor (Illumina) Refer to individual Series
2011-08-09 | E-GEOD-26736 | biostudies-arrayexpress
Project description:The CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Sequencing Project is a national, collaborative effort from 3 studies: Framingham Heart Study (FHS), Cardiovascular Health Study (CHS), and Atherosclerosis Risk in Communities (ARIC). It uses a case-cohort design, whereby a random sample of study participants is enriched with participants in extremes of traits. Although statistical methods are available to investigate the role of rare variants, few have evaluated their performance in a case-cohort design.We evaluate several methods, including the sequence kernel association test (SKAT), Score-Seq, and weighted (Madsen and Browning) and unweighted burden tests. Using genotypes from the CHARGE targeted-sequencing project for FHS (n = 1096), we simulate phenotypes in a large population for 11 correlated traits and then sample individuals to mimic the CHARGE Sequencing study design. We evaluate type I error and power for 77 targeted regions.We provide some guidelines on the performance of these aggregate-based tests to detect associations with rare variants when applied to case-cohort study designs, using CHARGE targeted sequencing data. Type I error is conservative when we consider variants with minor allele frequency (MAF) < 1%. Power is generally low, although it is relatively larger for Score-Seq. Greater numbers of causal variants and a greater proportion of variance improve the power, but it tends to be lower in the presence of bi-directionality of effects of causal genotypes, especially for Score-Seq.
| S-EPMC4197341 | biostudies-literature
Project description:BackgroundComparing metabolic profiles under different biological perturbations has become a powerful approach to investigating the functioning of cells. The profiles can be taken as single snapshots of a system, but more information is gained if they are measured longitudinally over time. The results are short time series consisting of relatively sparse data that cannot be analyzed effectively with standard time series techniques, such as autocorrelation and frequency domain methods. In this work, we study longitudinal time series profiles of glucose consumption in the yeast Saccharomyces cerevisiae under different temperatures and preconditioning regimens, which we obtained with methods of in vivo nuclear magnetic resonance (NMR) spectroscopy. For the statistical analysis we first fit several nonlinear mixed effect regression models to the longitudinal profiles and then used an ANOVA likelihood ratio method in order to test for significant differences between the profiles.ResultsThe proposed methods are capable of distinguishing metabolic time trends resulting from different treatments and associate significance levels to these differences. Among several nonlinear mixed-effects regression models tested, a three-parameter logistic function represents the data with highest accuracy. ANOVA and likelihood ratio tests suggest that there are significant differences between the glucose consumption rate profiles for cells that had been--or had not been--preconditioned by heat during growth. Furthermore, pair-wise t-tests reveal significant differences in the longitudinal profiles for glucose consumption rates between optimal conditions and heat stress, optimal and recovery conditions, and heat stress and recovery conditions (p-values <0.0001).ConclusionWe have developed a nonlinear mixed effects model that is appropriate for the analysis of sparse metabolic and physiological time profiles. The model permits sound statistical inference procedures, based on ANOVA likelihood ratio tests, for testing the significance of differences between short time course data under different biological perturbations.
| S-EPMC3114728 | biostudies-literature
Project description:With advances in medicine, many drugs and treatments become available. On the one hand, polydrug use (i.e. using more than one drug at a time) has been used to treat patients with multiple morbid conditions, and polydrug use may cause severe side effects. On the other hand, combination treatments have been successfully developed to treat severe diseases such as cancer and chronic diseases. Observational data, such as electronic health record data, may provide useful information for assessing drug interactions. In this article, we propose using marginal structural models to assess the average treatment effect and causal interaction of two drugs by controlling confounding variables. The causal effect and the interaction of two drugs are assessed using the weighted likelihood approach, with weights being the inverse probability of the treatment assigned. Simulation studies were conducted to examine the performance of the proposed method, which showed that the proposed method was able to estimate the causal parameters consistently. Case studies were conducted to examine the joint effect of metformin and glyburide use on reducing the hospital readmission for type 2 diabetic patients, and to examine the joint effect of antecedent statins and opioids use on the immune and inflammatory biomarkers for COVID-19 hospitalized patients.
| S-EPMC10810670 | biostudies-literature