Analyzing Efron’s BRCA data set

Introduction

It’s a classic microarray data set used many times by Efron to illustrate his “empirical null” idea. The data set is downloaded online

Sanity check

Pipeline can generate null \(z\) scores when it’s null?

brca.ratio <- read.table("../data/hedenfalk.txt", header = TRUE)
brca.logratio <- as.matrix(log2(brca.ratio[, c(1 : 6, 17, 7 : 10, 18 : 21)]))

Data analysis

source("../code/gdash_lik.R")
fit <- gdash(betahat, sebetahat)
cat(fit$w)

1 0.0363335 0.7005092 0.03116099 0.3066148 -0.02737636 2.826299e-08 -0.05660896 -6.044775e-09 -0.012571 5.774521e-10

sum(fit$qvalue <= 0.1)

[1] 0

Session information

sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

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_3.4.2  backports_1.1.1 magrittr_1.5    rprojroot_1.2  
 [5] tools_3.4.2     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.13   
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      git2r_0.19.0   
[13] stringr_1.2.0   digest_0.6.12   evaluate_0.10.1