Last updated: 2018-05-12

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    rmd 562cb28 LSun 2017-11-09 large-scale simulation

Introduction

We are doing large-scale simulation using CASH and other methods, with emphasis on the accuracy of FDR calibration.

All data sets on average, including both over-dispersion, under-dispersion, and else

source("../code/gdash_lik.R")
z.mat = readRDS("../output/z_null_liver_777.rds")
se.mat = readRDS("../output/sebetahat_null_liver_777.rds")

Expand here to see past versions of plot_pihat0-1.png:
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213e7e1 LSun 2017-11-10

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213e7e1 LSun 2017-11-10

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Expand here to see past versions of qvalue calibration plotting-2.png:
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213e7e1 LSun 2017-11-10

Session information

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ashr_2.2-2        Rmosek_8.0.69     PolynomF_1.0-1    CVXR_0.95        
[5] REBayes_1.2       Matrix_1.2-12     SQUAREM_2017.10-1 EQL_1.0-0        
[9] ttutils_1.0-1    

loaded via a namespace (and not attached):
 [1] gmp_0.5-13.1      Rcpp_0.12.16      compiler_3.4.3   
 [4] git2r_0.21.0      workflowr_1.0.1   R.methodsS3_1.7.1
 [7] R.utils_2.6.0     iterators_1.0.9   tools_3.4.3      
[10] digest_0.6.15     bit_1.1-12        evaluate_0.10.1  
[13] lattice_0.20-35   foreach_1.4.4     yaml_2.1.18      
[16] parallel_3.4.3    Rmpfr_0.6-1       ECOSolveR_0.4    
[19] stringr_1.3.0     knitr_1.20        rprojroot_1.3-2  
[22] bit64_0.9-7       grid_3.4.3        R6_2.2.2         
[25] rmarkdown_1.9     magrittr_1.5      whisker_0.3-2    
[28] MASS_7.3-47       backports_1.1.2   codetools_0.2-15 
[31] htmltools_0.3.6   scs_1.1-1         stringi_1.1.6    
[34] pscl_1.5.2        doParallel_1.0.11 truncnorm_1.0-7  
[37] R.oo_1.21.0

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