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Parametric Estimation of the Local False Discovery Rate for Identifying Genetic Associations
Jan.-Feb. 2013 (vol. 10 no. 1)
pp. 98-108
| ASCII Text | x | ||
| Ye Yang, Farnoosh Abbas Aghababazadeh, David R. Bickel, "Parametric Estimation of the Local False Discovery Rate for Identifying Genetic Associations," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 1, pp. 98-108, Jan.-Feb., 2013. | |||
| BibTex | x | ||
| @article{ 10.1109/TCBB.2012.140, author = {Ye Yang and Farnoosh Abbas Aghababazadeh and David R. Bickel}, title = {Parametric Estimation of the Local False Discovery Rate for Identifying Genetic Associations}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {10}, number = {1}, issn = {1545-5963}, year = {2013}, pages = {98-108}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.140}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, } | |||
| RefWorks Procite/RefMan/Endnote | x | ||
| TY - JOUR JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics TI - Parametric Estimation of the Local False Discovery Rate for Identifying Genetic Associations IS - 1 SN - 1545-5963 SP98 EP108 EPD - 98-108 A1 - Ye Yang, A1 - Farnoosh Abbas Aghababazadeh, A1 - David R. Bickel, PY - 2013 KW - Diseases KW - Solid modeling KW - Bioinformatics KW - Estimation KW - Adaptation models KW - Analytical models KW - Standards KW - strength of statistical evidence KW - Empirical Bayes KW - genome-wide association studies KW - local false discovery rate KW - minimum description length KW - MDL KW - reduced likelihood KW - Type II maximum likelihood VL - 10 JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics ER - | |||
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.140
Many genome-wide association studies have been conducted to identify single nucleotide polymorphisms (SNPs) that are associated with particular diseases or other traits. The local false discovery rate (LFDR) estimated using semiparametric models has enjoyed success in simultaneous inference. However, semiparametric LFDR estimators can be biased because they tend to overestimate the proportion of the nonassociated SNPs. We address the problem by adapting a simple parametric mixture model (PMM) and by comparing this model to the semiparametric mixture model (SMM) behind an LFDR estimator that is known to be conservatively biased. Then, we also compare the PMM with a parametric nonmixture model (PNM). In our simulation studies, we thoroughly analyze the performances of the three models under different values of $(p_{1})$, a prior probability that is approximately equal to the proportion of SNPs that are associated with the disease. When $(p_{1} > 10\%)$, the PMM generally performs better than the SMM. When $(p_{1} < 0.1\%)$, the SMM outperforms PMM. When $(p_{1})$ lies between 0.1 and 10 percent, both methods have about the same performance. In that setting, the PMM may be preferred since it has the advantage of supplying an estimate of the detectability level of the nonassociated SNPs.
Index Terms:
Diseases,Solid modeling,Bioinformatics,Estimation,Adaptation models,Analytical models,Standards,strength of statistical evidence,Empirical Bayes,genome-wide association studies,local false discovery rate,minimum description length,MDL,reduced likelihood,Type II maximum likelihood
Citation:
Ye Yang, Farnoosh Abbas Aghababazadeh, David R. Bickel, "Parametric Estimation of the Local False Discovery Rate for Identifying Genetic Associations," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 1, pp. 98-108, Jan.-Feb. 2013, doi:10.1109/TCBB.2012.140
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