Last updated: 2018-05-15

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Expand here to see past versions:
    File Version Author Date Message
    html e05bc83 LSun 2018-05-12 Update to 1.0
    rmd cc0ab83 Lei Sun 2018-05-11 update
    html 0f36d99 LSun 2017-12-21 Build site.
    html 853a484 LSun 2017-11-07 Build site.
    html aba8f90 LSun 2017-06-01 wflow
    html 2457dfb LSun 2017-06-01 simulations
    rmd e79fe80 LSun 2017-06-01 calibration plots
    html a29a916 LSun 2017-05-30 figures
    rmd 9101229 LSun 2017-05-30 large scale simulation

Introduction

Identifiability of small effects from correlation.

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

SNR = -10, Sparse mixture

\[g = 0.9\delta_0 + 0.1N\left(0, \sigma^2\right) \ .\]

Expand here to see past versions of -10 average fdp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

Expand here to see past versions of -10 average fsp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

SNR = -10, Sparse & strong

\[g = 0.99\delta_0 + 0.01N\left(0, \left(3.16\sigma\right)^2\right) \ .\]

Expand here to see past versions of -10S average fdp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

Expand here to see past versions of -10S average fsp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

SNR = -10, Dense & weak

\[g = 0.1\delta_0 + 0.9N\left(0, \left(0.33\sigma\right)^2\right) \ .\]

Expand here to see past versions of -10W average fdp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

Expand here to see past versions of -10W average fsp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

SNR = -3, Sparse mixture

\[g = 0.5\delta_0 + 0.5N\left(0, \sigma^2\right) \ .\]

Expand here to see past versions of -3 average fdp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

Expand here to see past versions of -3 average fsp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

SNR = -3, Sparse & strong

\[g = 0.6\delta_0 + 0.3N\left(0, \left(0.82\sigma\right)^2\right) + 0.1N\left(0, \left(1.73\sigma\right)^2\right) \ .\]

Expand here to see past versions of -3S average fdp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

Expand here to see past versions of -3S average fsp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

SNR = -3, Dense & weak

\[g = 0.1\delta_0 + 0.9N\left(0, \left(0.75\sigma^2\right)^2\right) \ .\]

Expand here to see past versions of -3W average fdp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

Expand here to see past versions of -3W average fsp plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
2457dfb LSun 2017-06-01

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