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Articles 31 - 40 of 40
Full-Text Articles in Statistical Models
Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes
Statistical Contributions To Proteomic Research, Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes
Jeffrey S. Morris
Proteomic profiling has the potential to impact the diagnosis, prognosis, and treatment of various diseases. A number of different proteomic technologies are available that allow us to look at many proteins at once, and all of them yield complex data that raise significant quantitative challenges. Inadequate attention to these quantitative issues can prevent these studies from achieving their desired goals, and can even lead to invalid results. In this chapter, we describe various ways the involvement of statisticians or other quantitative scientists in the study team can contribute to the success of proteomic research, and we outline some of the …
Informatics And Statistics For Analyzing 2-D Gel Electrophoresis Images, Andrew W. Dowsey, Jeffrey S. Morris, Howard G. Gutstein, Guang Z. Yang
Informatics And Statistics For Analyzing 2-D Gel Electrophoresis Images, Andrew W. Dowsey, Jeffrey S. Morris, Howard G. Gutstein, Guang Z. Yang
Jeffrey S. Morris
Whilst recent progress in ‘shotgun’ peptide separation by integrated liquid chromatography and mass spectrometry (LC/MS) has enabled its use as a sensitive analytical technique, proteome coverage and reproducibility is still limited and obtaining enough replicate runs for biomarker discovery is a challenge. For these reasons, recent research demonstrates the continuing need for protein separation by two-dimensional gel electrophoresis (2-DE). However, with traditional 2-DE informatics, the digitized images are reduced to symbolic data though spot detection and quantification before proteins are compared for differential expression by spot matching. Recently, a more robust and automated paradigm has emerged where gels are directly …
Bayesian Random Segmentationmodels To Identify Shared Copy Number Aberrations For Array Cgh Data, Veerabhadran Baladandayuthapani, Yuan Ji, Rajesh Talluri, Luis E. Nieto-Barajas, Jeffrey S. Morris
Bayesian Random Segmentationmodels To Identify Shared Copy Number Aberrations For Array Cgh Data, Veerabhadran Baladandayuthapani, Yuan Ji, Rajesh Talluri, Luis E. Nieto-Barajas, Jeffrey S. Morris
Jeffrey S. Morris
Array-based comparative genomic hybridization (aCGH) is a high-resolution high-throughput technique for studying the genetic basis of cancer. The resulting data consists of log fluorescence ratios as a function of the genomic DNA location and provides a cytogenetic representation of the relative DNA copy number variation. Analysis of such data typically involves estimation of the underlying copy number state at each location and segmenting regions of DNA with similar copy number states. Most current methods proceed by modeling a single sample/array at a time, and thus fail to borrow strength across multiple samples to infer shared regions of copy number aberrations. …
Bayesian Inference For A Periodic Stochastic Volatility Model Of Intraday Electricity Prices, Michael S. Smith
Bayesian Inference For A Periodic Stochastic Volatility Model Of Intraday Electricity Prices, Michael S. Smith
Michael Stanley Smith
The Gaussian stochastic volatility model is extended to allow for periodic autoregressions (PAR) in both the level and log-volatility process. Each PAR is represented as a first order vector autoregression for a longitudinal vector of length equal to the period. The periodic stochastic volatility model is therefore expressed as a multivariate stochastic volatility model. Bayesian posterior inference is computed using a Markov chain Monte Carlo scheme for the multivariate representation. A circular prior that exploits the periodicity is suggested for the log-variance of the log-volatilities. The approach is applied to estimate a periodic stochastic volatility model for half-hourly electricity prices …
Bayesian Skew Selection For Multivariate Models, Michael S. Smith, Anastasios Panagiotelis
Bayesian Skew Selection For Multivariate Models, Michael S. Smith, Anastasios Panagiotelis
Michael Stanley Smith
We develop a Bayesian approach for the selection of skew in multivariate skew t distributions constructed through hidden conditioning in the manners suggested by either Azzalini and Capitanio (2003) or Sahu, Dey and Branco~(2003). We show that the skew coefficients for each margin are the same for the standardized versions of both distributions. We introduce binary indicators to denote whether there is symmetry, or skew, in each dimension. We adopt a proper beta prior on each non-zero skew coefficient, and derive the corresponding prior on the skew parameters. In both distributions we show that as the degrees of freedom increases, …
Multilevel Functional Principal Component Analysis, Chong-Zhi Di, Ciprian M. Crainiceanu, Brian S. Caffo, Naresh M. Punjabi
Multilevel Functional Principal Component Analysis, Chong-Zhi Di, Ciprian M. Crainiceanu, Brian S. Caffo, Naresh M. Punjabi
Chongzhi Di
The Sleep Heart Health Study (SHHS) is a comprehensive landmark study of sleep and its impacts on health outcomes. A primary metric of the SHHS is the in-home polysomnogram, which includes two electroencephalographic (EEG) channels for each subject, at two visits. The volume and importance of this data presents enormous challenges for analysis. To address these challenges, we introduce multilevel functional principal component analysis (MFPCA), a novel statistical methodology designed to extract core intra- and inter-subject geometric components of multilevel functional data. Though motivated by the SHHS, the proposed methodology is generally applicable, with potential relevance to many modern scientific …
Nonparametric Signal Extraction And Measurement Error In The Analysis Of Electroencephalographic Activity During Sleep, Ciprian M. Crainiceanu, Brian S. Caffo, Chong-Zhi Di, Naresh M. Punjabi
Nonparametric Signal Extraction And Measurement Error In The Analysis Of Electroencephalographic Activity During Sleep, Ciprian M. Crainiceanu, Brian S. Caffo, Chong-Zhi Di, Naresh M. Punjabi
Chongzhi Di
We introduce methods for signal and associated variability estimation based on hierarchical nonparametric smoothing with application to the Sleep Heart Health Study (SHHS). SHHS is the largest electroencephalographic (EEG) collection of sleep-related data, which contains, at each visit, two quasi-continuous EEG signals for each subject. The signal features extracted from EEG data are then used in second level analyses to investigate the relation between health, behavioral, or biometric outcomes and sleep. Using subject specific signals estimated with known variability in a second level regression becomes a nonstandard measurement error problem.We propose and implement methods that take into account cross-sectional and …
Generalized Multilevel Functional Regression, Ciprian M. Crainiceanu, Ana-Maria Staicu, Chong-Zhi Di
Generalized Multilevel Functional Regression, Ciprian M. Crainiceanu, Ana-Maria Staicu, Chong-Zhi Di
Chongzhi Di
We introduce Generalized Multilevel Functional Linear Models (GMFLMs), a novel statistical framework for regression models where exposure has a multilevel functional structure. We show that GMFLMs are, in fact, generalized multilevel mixed models. Thus, GMFLMs can be analyzed using the mixed effects inferential machinery and can be generalized within a well-researched statistical framework. We propose and compare two methods for inference: (1) a two-stage frequentist approach; and (2) a joint Bayesian analysis. Our methods are motivated by and applied to the Sleep Heart Health Study, the largest community cohort study of sleep. However, our methods are general and easy to …
Additive Nonparametric Regression With Autocorrelated Errors, Michael S. Smith, C Wong, Robert Kohn
Additive Nonparametric Regression With Autocorrelated Errors, Michael S. Smith, C Wong, Robert Kohn
Michael Stanley Smith
A Bayesian approach is presented for nonparametric estimation of an additive regression model with autocorrelated errors. Each of the potentially nonlinear components is modelled as a regression spline using many knots, while the errors are modelled by a high order stationary autoregressive process parameterised in terms of its autocorrelations. The distribution of significant knots and partial autocorrelations is accounted for using subset selection. Our approach also allows the selection of a suitable transformation of the dependent variable. All aspects of the model are estimated simultaneously using Markov chain Monte Carlo. It is shown empirically that the proposed approach works well …
A Bayesian Approach To Additive Nonparametric Regression, Michael S. Smith, Robert Kohn
A Bayesian Approach To Additive Nonparametric Regression, Michael S. Smith, Robert Kohn
Michael Stanley Smith
This proceedings paper was the first to suggest using a Gaussian g-prior combined with a point mass to undertake Bayesian variable selection in a Gaussian linear regression model. It also was the first to suggest integrating out the regression parameters and variance in closed form, resulting in an efficient Gibbs sampling scheme. The idea was applied to estimate regression functions in an additive model by using a linear basis expansion for each component function in an additive model. The conference proceeding was eventually published in a slightly tighter form in Journal of Econometrics (1996).