Last updated: 2018-05-12

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    rmd cc0ab83 Lei Sun 2018-05-11 update
    html 0f36d99 LSun 2017-12-21 Build site.
    html 853a484 LSun 2017-11-07 Build site.
    html 043bf89 LSun 2017-11-05 transfer
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    rmd 4a210bb LSun 2017-07-21 wflow_publish(“analysis/brca.rmd”)
    rmd 4b385a1 LSun 2017-07-21 brca analysis
    html 4b385a1 LSun 2017-07-21 brca analysis

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 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

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] workflowr_1.0.1   Rcpp_0.12.16      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.21.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.1.6     whisker_0.3-2     R.oo_1.21.0      
[13] R.utils_2.6.0     rmarkdown_1.9     tools_3.4.3      
[16] stringr_1.3.0     yaml_2.1.18       compiler_3.4.3   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.0.1