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Controlling The False Discovery Rate - A Practical And Powerful Approach To Multiple Testing

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Abstract

The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses – the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferroni-type procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.
... The aim of this study was not to compare the brain-behavior relationships across the 3 racial/ethnic groups, but to generate associations that are inclusive and reproducible within races and ethnicities across the sample. The brain-behavior relationships were obtained from the strongest edge (R s ) in the functional connectome after applying the Benjamini-Hochberg False Discovery Rate (q = 0.05) 36 to correct for multiple comparisons across 61,776 edges (Supplementary Figure 2). While 17,854 edges shared a significant association with the NIH Toolbox, 65 edges yielded similar relationships with CBCL-externalizing. ...
... The standard, motion-ordered, and bagged brain-behavior associations were computed using the edge that produced the strongest R s in the functional connectome after surviving the Benjamini-Hochberg False Discovery Rate (q = 0.05) 36 . The strongest edges respectively had a correlation strength of |R s | = 0.20 for the NIH Toolbox and |R s | = 0.093 for the CBCL-externalizing. ...
... To detect the standard brain-behavior relationships across the low-motion youth, we computed the partial Spearman's Rank correlation (R s ) between functional connectivity and NIH Toolbox as well as CBCL externalizing and internalizing at the edge level using the full timeseries while adjusting for sex assigned at birth and head motion (indexed by mean FD). The edge that shared the strongest brain-behavior relationship (highest R s ) was selected after applying the Benjamini-Hochberg False Discovery Rate (q = 0.05) 36 to correct for multiple comparisons across 61,776 edges. The strongest R s was chosen based on its magnitude rather than sign to prevent penalizing negatively correlated edges (e.g., an edge's R s = -0.16 is stronger than another edge's R s = 0.15). ...
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Population neuroscience datasets allow researchers to estimate reliable effect sizes for brain-behavior associations because of their large sample sizes. However, these datasets undergo strict quality control to mitigate sources of noise, such as head motion. This practice often excludes a disproportionate number of minoritized individuals. We employ motion-ordering and motion-ordering+resampling (bagging) to test if these methods preserve functional MRI (fMRI) data in the Adolescent Brain Cognitive Development Study (N=5,733). Black and Hispanic youth exhibited excess head motion relative to data collected from White youth, and were discarded disproportionately when using conventional approaches. Both methods retained more than 99% of Black and Hispanic youth. They produced reproducible brain-behavior associations across low-/high-motion racial/ethnic groups based on motion-limited fMRI data. The motion-ordering and bagging methods are two feasible approaches that can enhance sample representation for testing brain-behavior associations and fulfill the promise of consortia datasets to produce generalizable effect sizes across diverse populations.
... The resulting distance matrices served as inputs for principal coordinates analysis (PCoA) and significance of sample clustering was analyzed by permutational multivariate analysis of variance (PERMANOVA) with 9,999 permutations. Regarding MaAsLin2, Benjamini-Hochberg FDR [86] adjusted Q-values < 0.1 were considered as significant. LEfSe uses a nonparametric factorial Kruskal Wallis and Wilcoxon rank sum test followed by a linear discriminate analysis to estimate the effect size of each taxon [78]. ...
... The variable importance in projection method (VIP) was Y ijk = µ + A i + P j + +T k + (PT) jk + ε ijk applied to assess the relevance of each metabolite considering the ordinary VIP ≥ 1.5 threshold, in order to identify the most important features. P values were corrected for FDR [86] and P < 0.05 and 0.05 ≤ P < 0.01 were considered as significant and tendency effects, respectively. Springer Nature journal content, brought to you courtesy of Springer Nature Customer Service Center GmbH ("Springer Nature"). ...
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... For vascular risk factors, we meta-analyzed the coefficients of the primary and secondary linear models. P-values were adjusted for multiple comparisons using Benjamini-Hochberg false discovery rate correction (FDR) with pFDR < 5% for inference [61]. 120 tests were included for vascular/genetic analyses, 64 cognitive and 40 for dementia/stroke analyses. ...
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INTRODUCTION: White matter hyperintensities (WMH), a major cerebral small vessel disease marker, may arise from different pathologies depending on their location. We explored clinical and genetic correlates of agnostically derived spatial WMH patterns in two longitudinal population-based cohorts (3C-Dijon, LIFE-Adult). METHODS: We derived seven WMH spatial patterns using Bullseye segmentation in 2,736 individuals aged 65+ and explored their associations with vascular and genetic risk factors, cognitive performance, dementia and stroke incidence. RESULTS: WMH in the fronto-parietal and anterior periventricular region were associated with blood pressure traits, WMH genetic risk score (GRS), baseline and decline in general cognitive performance, incident all-cause dementia and ischemic stroke. Juxtacortical-deep occipital WMH were not associated with vascular risk factors and WMH GRS, but with incident all-cause dementia and intracerebral hemorrhage. CONCLUSION: Accounting for WMH spatial distribution is key to decipher mechanisms underlying cerebral small vessel disease subtypes, an essential step towards personalized therapeutic approaches.
... Its standard deviation is determined as the median of LFQ intensity sample standard deviations calculated within and then averaged over each triplicate. Proteins were tested for differential expression using the limma package for the indicated pairwise comparison of samples and a Benjamini-Hochberg procedure was used to account for multiple testing (71). All relevant test results are listed in Table S4. ...
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