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.

Illustration

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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