Last updated: 2017-02-14

Code version: ab7e085

Introduction

We apply Benjamini–Hochberg’s FDR-controlling procedure, ash, and truncash (with the threshold \(T = 1.96\)) to the simulated, correlated null data, obtained from 5 vs 5 GTEx/Liver samples and 10K top expressed genes, and \(1000\) independent simulation trials. We compare the numbers of false discoveries (by definition, all discoveries will be false) obtained by these three methods, under FDR \(\leq 0.05\) and \(s\)-value \(\leq 0.05\) as cutoffs.

p = 1

Session Information

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

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] workflowr_0.3.0 rmarkdown_1.3   edgeR_3.14.0    limma_3.28.14  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9      codetools_0.2-15 digest_0.6.9     rprojroot_1.2   
 [5] backports_1.0.5  git2r_0.18.0     magrittr_1.5     evaluate_0.10   
 [9] stringi_1.1.2    tools_3.3.2      stringr_1.1.0    yaml_2.1.14     
[13] htmltools_0.3.5  knitr_1.15.1

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