Last updated: 2017-12-21
Code version: 6e42447
It’s a classic microarray data set used many times by Efron to illustrate his “empirical null” idea. The data set is downloaded online
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)]))
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
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
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