Diagnostic Plot for ASH

Introduction

Based on discussion with Matthew on several ideas to improve the diagnostic plot for ASH, this file documents the latest version of plot_diagnostic function in ashr.

library(ashr)

\(\alpha = 0.01\) rather than \(0.05\).

The idea is to “reduce the number of crossings some, but still give a good idea of what is expected without being too conservative.”

Other ideas

All have been put into the ashr::plot_diagnostic function.

Session information

sessionInfo()

R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.4

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] backports_1.0.5 magrittr_1.5    rprojroot_1.2   tools_3.3.3    
 [5] htmltools_0.3.5 yaml_2.1.14     Rcpp_0.12.10    stringi_1.1.2  
 [9] rmarkdown_1.3   knitr_1.15.1    git2r_0.18.0    stringr_1.2.0  
[13] digest_0.6.11   evaluate_0.10