A parametric bootstrap solution to the MANOVA under heteroscedasticity

Asymptotic-based bootstrap approach for matched pairs with missingness in a single arm

The issue of missing values is an arising difficulty when dealing with paired data. Several test procedures are developed in the literature to tackle this problem. Some of them are even robust under deviations and control type-I error quite accurately. However, most of these methods are not applicable when missing values are present only in a single arm. For this case, we provide asymptotic correct resampling tests that are robust under heteroskedasticity and skewed distributions. The tests are based on a meaningful restructuring of all observed information in quadratic form-type test statistics. An extensive simulation study is conducted exemplifying the tests for finite sample sizes under different missingness mechanisms. In addition, illustrative data examples based on real life studies are analyzed.

Combination rules for homoscedastic and heteroscedastic MANOVA models from multiply imputed datasets

Classical MANOVA tests do not pose any difficulty when the assumptions on which they are based are satisfied, while the modified Brown-Forsythe (MBF) procedure has low sensitivity to the lack of multivariate normality and homogeneity of covariance matrices. Both methods assume complete data for all subjects. In this paper, we present combination rules for the MANOVA and MBF procedures with multiply imputed datasets. These rules are illustrated by pooling the results obtained with a two-factor multivariate design after applying the two approaches to each of the imputed datasets when the covariance matrices were equal (MI-MANOVA) and when the covariance matrices were unequal (MI-MBF). A Monte-Carlo study was carried out to compare the proposed solution, in terms of type I error rates and statistical power, with the MANOVA and MBF approaches without missing data, and with listwise deletion of missing data followed by the MANOVA approach (LD-MANOVA) and listwise deletion followed by the MBF procedure (LD-MBF). Simulations showed that the type I error rates in all analyses on datasets with missing values (with or without imputation) were well controlled. We also found that the MI-MANOVA approach was substantially more powerful than LD-MANOVA. Moreover, the power of the MI-MANOVA was generally comparable to that of its complete data counterpart. Similar results were obtained for the MI-MBF procedure when covariance matrices were unequal. We conclude, based on the current evidence, that the solution presented performs well and could be of practical use. We illustrate the application of combination rules using a real dataset.

Integrating High-Throughput Phenotyping and Statistical Genomic Methods to Genetically Improve Longitudinal Traits in Crops

The rapid development of remote sensing in agronomic research allows the dynamic nature of longitudinal traits to be adequately described, which may enhance the genetic improvement of crop efficiency. For traits such as light interception, biomass accumulation, and responses to stressors, the data generated by the various high-throughput phenotyping (HTP) methods requires adequate statistical techniques to evaluate phenotypic records throughout time. As a consequence, information about plant functioning and activation of genes, as well as the interaction of gene networks at different stages of plant development and in response to environmental stimulus can be exploited. In this review, we outline the current analytical approaches in quantitative genetics that are applied to longitudinal traits in crops throughout development, describe the advantages and pitfalls of each approach, and indicate future research directions and opportunities.

Specificity of the metabolic signatures of fish from cyanobacteria rich lakes

With the increasing impact of the global warming, occurrences of cyanobacterial blooms in aquatic ecosystems are becoming a main worldwide ecological concern. Due to their capacity to produce potential toxic metabolites, interactions between the cyanobacteria, their cyanotoxins and the surrounding freshwater organisms have been investigated during the last past years. Non-targeted metabolomic analyses have the powerful capacity to study simultaneously a high number of metabolites and thus to investigate in depth the molecular signatures between various organisms encountering different environmental scenario, and potentially facing cyanobacterial blooms. In this way, the liver metabolomes of two fish species (Perca fluviatilis and Lepomis gibbosus) colonizing various peri-urban lakes of the Île-de-France region displaying high biomass of cyanobacteria, or not, were investigated. The fish metabolome hydrophilic fraction was analyzed by ¹H NMR analysis coupled with Batman peak treatment for the quantification and the annotation attempt of the metabolites. The results suggest that similar metabolome profiles occur in both fish species, for individuals collected from cyanobacterial blooming lakes compared to organism from non-cyanobacterial dominant environments. Overall, such environmental metabolomic pilot study provides new research perspectives in ecology and ecotoxicology fields, and may notably provide new information concerning the cyanobacteria/fish ecotoxicological interactions.

Testing Mean Differences among Groups: Multivariate and Repeated Measures Analysis with Minimal Assumptions

To date, there is a lack of satisfactory inferential techniques for the analysis of multivariate data in factorial designs, when only minimal assumptions on the data can be made. Presently available methods are limited to very particular study designs or assume either multivariate normality or equal covariance matrices across groups, or they do not allow for an assessment of the interaction effects across within-subjects and between-subjects variables. We propose and methodologically validate a parametric bootstrap approach that does not suffer from any of the above limitations, and thus provides a rather general and comprehensive methodological route to inference for multivariate and repeated measures data. As an example application, we consider data from two different Alzheimer's disease (AD) examination modalities that may be used for precise and early diagnosis, namely, single-photon emission computed tomography (SPECT) and electroencephalogram (EEG). These data violate the assumptions of classical multivariate methods, and indeed classical methods would not have yielded the same conclusions with regards to some of the factors involved.