Ir al contenido

Documat


False discovery rate control for grouped or discretely supported p-values with application to a neuroimaging study

  • Autores: Hien Nguyen, Yohan Yee, Geoffrey J. McLachlan, Jason Lerch
  • Localización: Sort: Statistics and Operations Research Transactions, ISSN 1696-2281, Vol. 43, Nº. 2, 2019, págs. 237-258
  • Idioma: inglés
  • Enlaces
  • Resumen
    • False discovery rate (FDR) control is important in multiple testing scenarios that are common in neuroimaging experiments, and p-values from such experiments may often arise from some discretely supported distribution or may be grouped in some way. Two situations that may lead to discretely supported distributions are when the p-values arise from Monte Carlo or permutation tests are used. Grouped p-values may occur when p-values are quantized for storage. In the neuroimaging context, grouped p-values may occur when data are stored in an integer-encoded form. We present a method for FDR control that is applicable in cases where only p-values are available for inference, and when those p-values are discretely supported or grouped. We assess our method via a comprehensive set of simulation scenarios and find that our method can outperform commonly used FDR control schemes in various cases. An implementation to a mouse imaging data set is used as an example to demonstrate the applicability of our approach.

  • Referencias bibliográficas
    • Alexander-Bloch, A., Giedd, J. N. and Bullmore, E. (2013). Imaging structural co-variance between human brain regions. Nature Reviews Neuroscience,...
    • Amemiya, T. (1985). Advanced Econometrics. Cambridge: Harvard University Press.
    • Ashburner, J. and Friston, K. J. (2000). Voxel-based morphometry—the methods. NeuroImage, 11, 805– 821.
    • Barreto, H. and Howland, F. M. (2006). Introductory Econometrics Using Monte Carlo Simulation with Microsoft Excel. Cambridge: Cambridge University...
    • Benaglia, T., Chauveau, D., Hunter, D. R. and Young, D. S. (2009). mixtools: An R package for analyzing finite mixture models. Journal of...
    • Benjamini, Y. (2010). Discovering the false discovery rate. Journal of the Royal Statistical Society B, 72, 405–416.
    • Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal...
    • Benjamini, Y. and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. Annals of Statistics,...
    • Bennett, C. M., Baird, A. A., Miller, M. B. and Wolford, G. L. (2009). Neuro correlates of interspecies perspective taking in the post-mortem...
    • Bidgood, W. D., Horri, S. C., Prior, F. W. and Van Syckle, D. E. (1997). Understanding and using DICOM, the data interchange standard for...
    • Birge, L. and Rozenholc, Y. (2006). How many bins should be put in a regular histogram. ESAIM: Probability and Statistics, 10, 24–45.
    • Cox, R. W., Ashburner, J., Breman, H., Fissell, K., Haselgrove, C., Holmes, C. J., Lancaster, J. L., Rex, D. E., Smith, S. M., Woodward, J....
    • Dempster, A. P., Laird, N. M. and Rubin, D. B. (1977). Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal...
    • Denby, L. and Mallows, C. (2009). Variations on the histogram. Journal of Computational and Graphical Statistics, 18, 21–31.
    • Dickhaus, T. (2014). Simultaneous Statistical Inference: With Applications in the Life Sciences. New York: Springer.
    • Dong, H.-W., Pretrovich, G. D., Watts, A. G. and Swanson, L. W. (2001). Basic organization of projections from the oval and fusiform nuclei...
    • Dong, H.-W. and Swanson, L. R. (2006). Projections from bed nuclei of the stria terminalis, anteromedial area: cerebral hemisphere integration...
    • Efron, B. (2004). Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. Journal of the American Statistical Association,...
    • Efron, B. (2010). Large-scale Inference. Cambridge: Cambridge University Press. https://github.com/hiendn/FDR_for_grouped_P_values
    • Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment. Journal of the American...
    • Ellegood, J., Anagnostou, E., Babineau, B., Crawley, J., Lin, L., Genestine, M., Dicicco-Bloom, E., Lai, J.,
    • Foster, J., Penagarikano, O., Geshwind, H., Pacey, L. K., Hampson, D. R., Laliberte, C. L., Mills, A. A., Tam, E., Osborne, L. R., Kouser,...
    • Evans, A. C. (2013). Networks of anatomical covariance. Neuroimage, 80, 489–504.
    • Fisher, R. A. (1921). On the “probable error” of a coefficient of correlation deduced from a small sample. Metron, 1, 3–32.
    • Freedman, D. and Diaconis, P. (1981). On the histogram as a density estimator: L2 theory. Zeitschrift fur Wahrscheinlichkeitstheorie und verwandte...
    • Genovese, C. R., Lazar, N. A. and Nichols, T. (2002). Thresholding of statistical maps in functional neuroimaging using the false discovery...
    • Gersho, A. and Gray, R. M. (1992). Vector Quantization and Signal Compression. New York: Springer.
    • Habiger, J. D. and Pena, E. A. (2011). Randomised P-values and nonparametric procedures in multiple testing. Journal of Nonparametric Statistics,...
    • Kontkanen, P. and Myllymaki, P. (2007). MDL histogram density estimation. In Artificial Intelligence and Statistics (pp. 219–226).
    • Korn, E. L., Troendle, J. F., McShane, L. M. and Simon, R. (2004). Controlling the number of false discoveries: application to high-dimensional...
    • Larobina, M. and Murino, L. (2014). Medical image file formats. Journal of Digital Imaging, 27, 200–206.
    • Lerch, J. P., Sled, J. G. and Henkelman, R. M. (2010). Magnetic Resonance Neuroimaging, chapter MRI phenotyping of genetically altered mice,...
    • Lerch, J. P., Worsley, K., Shaw, W. P., Greenstein, D. K., Lenroot, K. L., Giedd, J. and Evans, A. C. (2006). Mapping anatomic correlations...
    • Li, X., Pu, F., Fan, Y., Niu, H., Li, S. and Li, D. (2013). Age-related changes in brain structural covariance networks. Frontiers in Human...
    • MacDonald, P. D. M. and Du, J. (2012). mixdist: Finite Mixture Distribution Models. Comprehensive R Archive Network.
    • McLachlan, G. J., Bean, R. W. and Ben-Tovim Jones, L. (2006). A simple implementation of a normal mixture approach to differential gene expression...
    • McLachlan, G. J. and Jones, P. N. (1988). Fitting mixture models to grouped and truncated data via the EM algorithm. Biometrics, 44, 571–578.
    • McMenamin, B. W. and Pessoa, L. (2015). Discovering networks altered by potential threat (”anxiety”) using quadratic discriminant analysis....
    • Moschitta, A., Schoukens, J. and Carbone, P. (2015). Information and statistical efficiency when quantizing noisy DC values. IEEE Transactions...
    • Nguyen, H. D., McLachlan, G. J., Cherbuin, N. and Janke, A. L. (2014). False discovery rate control in magnetic resonance imaging studies...
    • Pagani, M., Bifone, A. and Gozzi, A. (2016). Structural covariance networks in the mouse brain. Neuroimage, 129, 55–63.
    • Perlmutter, S. M., Cosman, P. C., Tseng, C.-W., Olshen, R. A., Grey, R. M., Li, K. C. P. and Bergin, C. J. (1998). Medical image compression...
    • Phipson, B. and Smyth, G. K. (2010). Permutation p-values should never be zero: calculating exact pvalues whenn permutations are randomly...
    • Pollard, C. S. and van der Laan, M. J. (2004). Choice of a null distribution in resampling-based multiple testing. Statistical Planning and...
    • R Core Team (2016). R: a language and environment for statistical computing. R Foundation for Statistical Computing.
    • Raznahan, A., Lerch, J. P., Lee, N., Greenstein, D., Wallace, G. L., Stockman, M., Clasen, L., Shaw, P. W. and Giedd, J. N. (2011). Patterns...
    • Robb, R. A., Hanson, D. P., Karwoski, R. A., Larson, A. G., Workman, E. L. and Stacy, M. C. (1989). Analyze: a comprehensive, operator-interactive...
    • Scott, D. W. (1979). On optimal and data-based histograms. Biometrika, 66, 605–610.
    • Seeley, W. W., Zhou, R. K. C. J., Miller, B. L. and Greicius, M. D. (2009). Neurodegenerative diseases target large-scale human brain networks....
    • Sharda, M., Khundrakpam, B. S., Evans, A. C. and Singh, N. C. (2016). Disruption of structural covariance networks for language in autism...
    • Sled, J. G., Zijdenbos, A. P. and Evans, A. C. (1998). A nonparametric method for automatic correction of intensity nonuniformity in MRI data....
    • Storey, J. D. (2002). A direct approach to false discovery rates. Journal of the Royal Statistical Society Series B, 64, 479–498.
    • Storey, J. D., Bass, A. J., Dabney, A. and Robinson, D. (2015). qvalue: Q-value estimation for false discovery rate control.
    • Sturges, H. A. (1926). The choice of a class interval. Journal of the American Statistical Association, 21, 65–66.
    • Torrisi, S., O’Connell, K., Davis, A., Reynolds, R., Balderston, N., Fudge, J. L., Grillon, C. and Ernst, M. (2015). Resting state connectivity...
    • Turnbull, B. W. (1976). The empirical distribution function with arbitrarily grouped, censored and truncated data. Journal of the Royal Statistical...
    • van der Laan, M. J. and Hubbard, A. E. (2006). Quantile-function based null distribution in resampling based multiple testing. Statistical...
    • Varin, C. (2008). On composite marginal likelihoods. Advances in Statistical Analysis, 92, 1–28.
    • Vincent, R. D., Janke, A., Sled, J. G., Baghdadi, L., Neelin, P. and Evans, A. C. (2003). MINC 2.0: a modality independent format for multidimensional...
    • Wand, M. P. (1997). Data-Based Choice of Histogram Bin Width. The American Statistician, 51, 59–64.
    • Wheeler, A. L. and Voineskos, A. N. (2014). A review of structural neuroimaging in schizophrenia: from connectivity to connectomics. Frontiers...
    • White, H. (1982). Maximum likelihood estimation of misspecified models. Econometrica, 50, 1–25.
    • Winkler, A. M., Ridgway, G. R., Webster, M. A., Smith, S. M. and Nichols, T. E. (2014). Permutation inference for the general linear model....
    • Yekutieli, D. and Benjamini, Y. (1999). Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics....

Fundación Dialnet

Mi Documat

Opciones de artículo

Opciones de compartir

Opciones de entorno