Large-scale simulation for the cash paper, Part 2: Over-dispersion

Conditioned on over-dispersed data sets only

source("../code/gdash_lik.R")

z.mat = readRDS("../output/z_null_liver_777.rds")
se.mat = readRDS("../output/sebetahat_null_liver_777.rds")

z.sd <- apply(z.mat, 1, sd)
inflation.index = (z.sd > qchisq(0.9995, ncol(z.mat) - 1) / (ncol(z.mat) - 1))
deflation.index = (z.sd < qchisq(0.0005, ncol(z.mat) - 1) / (ncol(z.mat) - 1))
## Number of inflation data sets
sum(inflation.index)

[1] 299

## Number of deflation data sets
sum(deflation.index)

[1] 477

z.mat = z.mat[inflation.index, ]
se.mat = se.mat[inflation.index, ]

Session information

sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

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_2.1-27       Rmosek_7.1.3      PolynomF_0.94     cvxr_0.0.0.9400  
[5] REBayes_0.85      Matrix_1.2-11     SQUAREM_2017.10-1 EQL_1.0-0        
[9] ttutils_1.0-1    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13      knitr_1.17        magrittr_1.5     
 [4] MASS_7.3-47       pscl_1.5.2        doParallel_1.0.11
 [7] lattice_0.20-35   foreach_1.4.3     stringr_1.2.0    
[10] tools_3.4.2       parallel_3.4.2    grid_3.4.2       
[13] git2r_0.19.0      iterators_1.0.8   htmltools_0.3.6  
[16] yaml_2.1.14       rprojroot_1.2     digest_0.6.12    
[19] gmp_0.5-13.1      codetools_0.2-15  evaluate_0.10.1  
[22] rmarkdown_1.6     stringi_1.1.5     compiler_3.4.2   
[25] backports_1.1.1   truncnorm_1.0-7