Last updated: 2018-05-12

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    html beb4122 LSun 2017-05-30 real data simulation
    rmd 7e6560b LSun 2017-05-30 real data simulation

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, and \(100\) independent simulation trials.

ngene = 1e4
N = 100

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

nsamp = 4
pi0 = 0.9
sd = 1
set.seed(777)
system.time(gdash.comp <- N_simulations(N, mat, nsamp, ngene, pi0, sd))
Coefficients not estimable: 3 
Warning: Partial NA coefficients for 10000 probe(s)
Warning in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
stdev.coef.lim, : Estimation of var.prior failed - set to default value
Warning: Zero sample variances detected, have been offset
Coefficients not estimable: 3 
Warning: Partial NA coefficients for 10000 probe(s)
Warning in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
stdev.coef.lim, : Estimation of var.prior failed - set to default value
Coefficients not estimable: 3 
Warning: Partial NA coefficients for 10000 probe(s)

Warning: Estimation of var.prior failed - set to default value
    user   system  elapsed 
4082.811  380.118 1649.864

Setting 2: \(3\) v \(3\), \(\pi_0 = 0.9\), \(\sigma^2 = 1\)

nsamp = 6
pi0 = 0.9
sd = 1
set.seed(777)
system.time(gdash.comp <- N_simulations(N, mat, nsamp, ngene, pi0, sd))
    user   system  elapsed 
4235.948  319.028 1655.836

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     

loaded via a namespace (and not attached):
 [1] workflowr_1.0.1   Rcpp_0.12.16      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.21.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.1.6     whisker_0.3-2     R.oo_1.21.0      
[13] R.utils_2.6.0     rmarkdown_1.9     tools_3.4.3      
[16] stringr_1.3.0     yaml_2.1.18       compiler_3.4.3   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.0.1