Last updated: 2017-06-01

Code version: a40ffff

library(ashr)
library(edgeR)
library(limma)
library(pROC)
source("../code/gdash.R")

Read in data

data = readRDS("../data/liver.rds")
ngene = 1e4
data = top_gene_selection(ngene, data)$data

Global Null

\[ g \equiv 0 \ . \]

SNR = 0

\[ g = 0.6\delta_0 + 0.3N\left(0, \sigma^2\right) + 0.1N\left(0, \left(2.65\sigma\right)^2\right) \ . \]

SNR = 2

\[ g = 0.6\delta_0 + 0.3N\left(0, \sigma^2\right) + 0.1N\left(0, \left(3.58\sigma\right)^2\right) \ . \]

SNR = 5

\[ g = 0.6\delta_0 + 0.3N\left(0, \left(2\sigma\right)^2\right) + 0.1N\left(0, \left(4.43\sigma\right)^2\right) \ . \]

SNR = 10

\[ g = 0.6\delta_0 + 0.3N\left(0, \left(3\sigma\right)^2\right) + 0.1N\left(0, \left(8.54\sigma\right)^2\right) \ . \]

Session information

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.5

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] Rmosek_7.1.2      PolynomF_0.94     cvxr_0.0.0.9009  
 [4] REBayes_0.85      Matrix_1.2-10     SQUAREM_2016.10-1
 [7] EQL_1.0-0         ttutils_1.0-1     pROC_1.9.1       
[10] edgeR_3.14.0      limma_3.28.21     ashr_2.1-13      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10      knitr_1.16        magrittr_1.5     
 [4] MASS_7.3-47       doParallel_1.0.10 pscl_1.4.9       
 [7] lattice_0.20-35   foreach_1.4.3     plyr_1.8.4       
[10] stringr_1.2.0     tools_3.3.3       parallel_3.3.3   
[13] grid_3.3.3        git2r_0.18.0      htmltools_0.3.6  
[16] iterators_1.0.8   yaml_2.1.14       rprojroot_1.2    
[19] digest_0.6.12     codetools_0.2-15  evaluate_0.10    
[22] rmarkdown_1.5     stringi_1.1.5     backports_1.0.5  
[25] truncnorm_1.0-7

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