Real Data with Simulated Signals: Part III

Introduction

We are comparing our method with ASH and SVA.

library(ashr)
library(edgeR)
library(limma)
library(seqgendiff)
library(sva)
library(pROC)

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

Artefactual effects \(\pi_0\delta_0 + \left(1 - \pi_0\right)N\left(0, \sigma^2\right)\) are added to the real GTEx data.

mat = read.csv("../data/liver.csv")

We are using \(10K\) genes, \(5\) v \(5\) experimental design, and \(100\) independent simulation trials.

ngene = 1e4
nsamp = 10
N = 100

Setting 1: \(\pi_0 = 0.9\), \(\sigma^2 = 1\)

pi0 = 0.9
sd = 1
set.seed(777)
system.time(gdash.comp <- N_simulations(N, mat, nsamp, ngene, pi0, sd))

     user    system   elapsed 
18421.805  1175.855  3889.120 

Setting 2: \(\pi_0 = 0.9\), \(\sigma^2 = 2\)

pi0 = 0.9
sd = sqrt(2)
set.seed(777)
system.time(gdash.comp <- N_simulations(N, mat, nsamp, ngene, pi0, sd))

     user    system   elapsed 
19523.364  1271.100  4140.141 

Setting 3: \(\pi_0 = 0.9\), \(\sigma^2 = 3\)

pi0 = 0.9
sd = sqrt(3)
set.seed(777)
system.time(gdash.comp <- N_simulations(N, mat, nsamp, ngene, pi0, sd))

     user    system   elapsed 
17770.699  1169.506  3854.622 

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 10.13.2

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     

loaded via a namespace (and not attached):
 [1] compiler_3.4.3  backports_1.1.2 magrittr_1.5    rprojroot_1.3-1
 [5] tools_3.4.3     htmltools_0.3.6 yaml_2.1.16     Rcpp_0.12.14   
 [9] stringi_1.1.6   rmarkdown_1.8   knitr_1.17      git2r_0.20.0   
[13] stringr_1.2.0   digest_0.6.13   evaluate_0.10.1