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Minimum Description Length Measures Of Evidence For Enrichment, Zhenyu Yang, David R. Bickel
Minimum Description Length Measures Of Evidence For Enrichment, Zhenyu Yang, David R. Bickel
COBRA Preprint Series
In order to functionally interpret differentially expressed genes or other discovered features, researchers seek to detect enrichment in the form of overrepresentation of discovered features associated with a biological process. Most enrichment methods treat the p-value as the measure of evidence using a statistical test such as the binomial test, Fisher's exact test or the hypergeometric test. However, the p-value is not interpretable as a measure of evidence apart from adjustments in light of the sample size. As a measure of evidence supporting one hypothesis over the other, the Bayes factor (BF) overcomes this drawback of the p-value but lacks …
Powerful Snp Set Analysis For Case-Control Genome Wide Association Studies, Michael C. Wu, Peter Kraft, Michael P. Epstein, Deanne M. Taylor, Stephen J. Chanock, David J. Hunter, Xihong Lin
Powerful Snp Set Analysis For Case-Control Genome Wide Association Studies, Michael C. Wu, Peter Kraft, Michael P. Epstein, Deanne M. Taylor, Stephen J. Chanock, David J. Hunter, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
Sparse Linear Discriminant Analysis For Simultaneous Testing For The Significance Of A Gene Set/Pathway And Gene Selection, Michael C. Wu, Lingson Zhang, Zhaoxi Wang, David C. Christiani, Xihong Lin
Sparse Linear Discriminant Analysis For Simultaneous Testing For The Significance Of A Gene Set/Pathway And Gene Selection, Michael C. Wu, Lingson Zhang, Zhaoxi Wang, David C. Christiani, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
Estimation And Testing For The Effect Of A Genetic Pathway On A Disease Outcome Using Logistic Kernel Machine Regression Via Logistic Mixed Models, Dawei Liu, Debashis Ghosh, Xihong Lin
Estimation And Testing For The Effect Of A Genetic Pathway On A Disease Outcome Using Logistic Kernel Machine Regression Via Logistic Mixed Models, Dawei Liu, Debashis Ghosh, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
A Powerful And Flexible Multilocus Association Test For Quantitative Traits, Lydia Coulter Kwee, Dawei Liu, Xihong Lin, Debashis Ghosh, Michael P. Epstein
A Powerful And Flexible Multilocus Association Test For Quantitative Traits, Lydia Coulter Kwee, Dawei Liu, Xihong Lin, Debashis Ghosh, Michael P. Epstein
Harvard University Biostatistics Working Paper Series
No abstract provided.
Assessing Population Level Genetic Instability Via Moving Average, Samuel Mcdaniel, Rebecca Betensky, Tianxi Cai
Assessing Population Level Genetic Instability Via Moving Average, Samuel Mcdaniel, Rebecca Betensky, Tianxi Cai
Harvard University Biostatistics Working Paper Series
No abstract provided.
Assessment Of A Cgh-Based Genetic Instability, David A. Engler, Yiping Shen, J F. Gusella, Rebecca A. Betensky
Assessment Of A Cgh-Based Genetic Instability, David A. Engler, Yiping Shen, J F. Gusella, Rebecca A. Betensky
Harvard University Biostatistics Working Paper Series
No abstract provided.
Survival Analysis With Large Dimensional Covariates: An Application In Microarray Studies, David A. Engler, Yi Li
Survival Analysis With Large Dimensional Covariates: An Application In Microarray Studies, David A. Engler, Yi Li
Harvard University Biostatistics Working Paper Series
Use of microarray technology often leads to high-dimensional and low- sample size data settings. Over the past several years, a variety of novel approaches have been proposed for variable selection in this context. However, only a small number of these have been adapted for time-to-event data where censoring is present. Among standard variable selection methods shown both to have good predictive accuracy and to be computationally efficient is the elastic net penalization approach. In this paper, adaptation of the elastic net approach is presented for variable selection both under the Cox proportional hazards model and under an accelerated failure time …
Power Boosting In Genome-Wide Studies Via Methods For Multivariate Outcomes, Mary J. Emond
Power Boosting In Genome-Wide Studies Via Methods For Multivariate Outcomes, Mary J. Emond
UW Biostatistics Working Paper Series
Whole-genome studies are becoming a mainstay of biomedical research. Examples include expression array experiments, comparative genomic hybridization analyses and large case-control studies for detecting polymorphism/disease associations. The tactic of applying a regression model to every locus to obtain test statistics is useful in such studies. However, this approach ignores potential correlation structure in the data that could be used to gain power, particularly when a Bonferroni correction is applied to adjust for multiple testing. In this article, we propose using regression techniques for misspecified multivariate outcomes to increase statistical power over independence-based modeling at each locus. Even when the outcome …
Semiparametric Regression Of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines And Linear Mixed Models, Dawei Liu, Xihong Lin, Debashis Ghosh
Semiparametric Regression Of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines And Linear Mixed Models, Dawei Liu, Xihong Lin, Debashis Ghosh
Harvard University Biostatistics Working Paper Series
No abstract provided.
Structural Inference In Transition Measurement Error Models For Longitudinal Data, Wenqin Pan, Xihong Lin, Donglin Zeng
Structural Inference In Transition Measurement Error Models For Longitudinal Data, Wenqin Pan, Xihong Lin, Donglin Zeng
Harvard University Biostatistics Working Paper Series
No abstract provided.
Nonparametric Regression Using Local Kernel Estimating Equations For Correlated Failure Time Data, Zhangsheng Yu, Xihong Lin
Nonparametric Regression Using Local Kernel Estimating Equations For Correlated Failure Time Data, Zhangsheng Yu, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
Causal Inference In Hybrid Intervention Trials Involving Treatment Choice, Qi Long, Rod Little, Xihong Lin
Causal Inference In Hybrid Intervention Trials Involving Treatment Choice, Qi Long, Rod Little, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
A Comparison Of Methods For Estimating The Causal Effect Of A Treatment In Randomized Clinical Trials Subject To Noncompliance, Rod Little, Qi Long, Xihong Lin
A Comparison Of Methods For Estimating The Causal Effect Of A Treatment In Randomized Clinical Trials Subject To Noncompliance, Rod Little, Qi Long, Xihong Lin
Harvard University Biostatistics Working Paper Series
No abstract provided.
New Statistical Paradigms Leading To Web-Based Tools For Clinical/Translational Science, Knut M. Wittkowski
New Statistical Paradigms Leading To Web-Based Tools For Clinical/Translational Science, Knut M. Wittkowski
COBRA Preprint Series
As the field of functional genetics and genomics is beginning to mature, we become confronted with new challenges. The constant drop in price for sequencing and gene expression profiling as well as the increasing number of genetic and genomic variables that can be measured makes it feasible to address more complex questions. The success with rare diseases caused by single loci or genes has provided us with a proof-of-concept that new therapies can be developed based on functional genomics and genetics.
Common diseases, however, typically involve genetic epistasis, genomic pathways, and proteomic pattern. Moreover, to better understand the underlying biologi-cal …