Last updated: 2018-05-12

workflowr checks: (Click a bullet for more information)
  • R Markdown file: up-to-date

    Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

  • Environment: empty

    Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

  • Seed: set.seed(12345)

    The command set.seed(12345) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

  • Session information: recorded

    Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

  • Repository version: ddf9062

    Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

    Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
    
    Ignored files:
        Ignored:    .DS_Store
        Ignored:    .Rhistory
        Ignored:    .Rproj.user/
        Ignored:    analysis/.DS_Store
        Ignored:    analysis/BH_robustness_cache/
        Ignored:    analysis/FDR_Null_cache/
        Ignored:    analysis/FDR_null_betahat_cache/
        Ignored:    analysis/Rmosek_cache/
        Ignored:    analysis/StepDown_cache/
        Ignored:    analysis/alternative2_cache/
        Ignored:    analysis/alternative_cache/
        Ignored:    analysis/ash_gd_cache/
        Ignored:    analysis/average_cor_gtex_2_cache/
        Ignored:    analysis/average_cor_gtex_cache/
        Ignored:    analysis/brca_cache/
        Ignored:    analysis/cash_deconv_cache/
        Ignored:    analysis/cash_fdr_1_cache/
        Ignored:    analysis/cash_fdr_2_cache/
        Ignored:    analysis/cash_fdr_3_cache/
        Ignored:    analysis/cash_fdr_4_cache/
        Ignored:    analysis/cash_fdr_5_cache/
        Ignored:    analysis/cash_fdr_6_cache/
        Ignored:    analysis/cash_plots_cache/
        Ignored:    analysis/cash_sim_1_cache/
        Ignored:    analysis/cash_sim_2_cache/
        Ignored:    analysis/cash_sim_3_cache/
        Ignored:    analysis/cash_sim_4_cache/
        Ignored:    analysis/cash_sim_5_cache/
        Ignored:    analysis/cash_sim_6_cache/
        Ignored:    analysis/cash_sim_7_cache/
        Ignored:    analysis/correlated_z_2_cache/
        Ignored:    analysis/correlated_z_3_cache/
        Ignored:    analysis/correlated_z_cache/
        Ignored:    analysis/create_null_cache/
        Ignored:    analysis/cutoff_null_cache/
        Ignored:    analysis/design_matrix_2_cache/
        Ignored:    analysis/design_matrix_cache/
        Ignored:    analysis/diagnostic_ash_cache/
        Ignored:    analysis/diagnostic_correlated_z_2_cache/
        Ignored:    analysis/diagnostic_correlated_z_3_cache/
        Ignored:    analysis/diagnostic_correlated_z_cache/
        Ignored:    analysis/diagnostic_plot_2_cache/
        Ignored:    analysis/diagnostic_plot_cache/
        Ignored:    analysis/efron_leukemia_cache/
        Ignored:    analysis/fitting_normal_cache/
        Ignored:    analysis/gaussian_derivatives_2_cache/
        Ignored:    analysis/gaussian_derivatives_3_cache/
        Ignored:    analysis/gaussian_derivatives_4_cache/
        Ignored:    analysis/gaussian_derivatives_5_cache/
        Ignored:    analysis/gaussian_derivatives_cache/
        Ignored:    analysis/gd-ash_cache/
        Ignored:    analysis/gd_delta_cache/
        Ignored:    analysis/gd_lik_2_cache/
        Ignored:    analysis/gd_lik_cache/
        Ignored:    analysis/gd_w_cache/
        Ignored:    analysis/knockoff_10_cache/
        Ignored:    analysis/knockoff_2_cache/
        Ignored:    analysis/knockoff_3_cache/
        Ignored:    analysis/knockoff_4_cache/
        Ignored:    analysis/knockoff_5_cache/
        Ignored:    analysis/knockoff_6_cache/
        Ignored:    analysis/knockoff_7_cache/
        Ignored:    analysis/knockoff_8_cache/
        Ignored:    analysis/knockoff_9_cache/
        Ignored:    analysis/knockoff_cache/
        Ignored:    analysis/knockoff_var_cache/
        Ignored:    analysis/marginal_z_alternative_cache/
        Ignored:    analysis/marginal_z_cache/
        Ignored:    analysis/mosek_reg_2_cache/
        Ignored:    analysis/mosek_reg_4_cache/
        Ignored:    analysis/mosek_reg_5_cache/
        Ignored:    analysis/mosek_reg_6_cache/
        Ignored:    analysis/mosek_reg_cache/
        Ignored:    analysis/pihat0_null_cache/
        Ignored:    analysis/plot_diagnostic_cache/
        Ignored:    analysis/poster_obayes17_cache/
        Ignored:    analysis/real_data_simulation_2_cache/
        Ignored:    analysis/real_data_simulation_3_cache/
        Ignored:    analysis/real_data_simulation_4_cache/
        Ignored:    analysis/real_data_simulation_5_cache/
        Ignored:    analysis/real_data_simulation_cache/
        Ignored:    analysis/rmosek_primal_dual_2_cache/
        Ignored:    analysis/rmosek_primal_dual_cache/
        Ignored:    analysis/seqgendiff_cache/
        Ignored:    analysis/simulated_correlated_null_2_cache/
        Ignored:    analysis/simulated_correlated_null_3_cache/
        Ignored:    analysis/simulated_correlated_null_cache/
        Ignored:    analysis/simulation_real_se_2_cache/
        Ignored:    analysis/simulation_real_se_cache/
        Ignored:    analysis/smemo_2_cache/
        Ignored:    data/LSI/
        Ignored:    docs/.DS_Store
        Ignored:    docs/figure/.DS_Store
        Ignored:    output/fig/
    
    Unstaged changes:
        Deleted:    analysis/cash_plots_fdp.Rmd
    
    
    Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
Expand here to see past versions:
    File Version Author Date Message
    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 0214a4b LSun 2017-06-16 data transfer
    html c5c229c LSun 2017-05-20 figures
    rmd 700fba8 LSun 2017-05-20 real data analysis

Introduction

We are comparing our method with ASH and SVA.

library(ashr)
library(edgeR)
library(limma)
library(seqgendiff)
library(sva)
library(pROC)
source("../code/gdash.R")

Artefactual effects \(\pi_0\delta_0 + \left(1 - \pi_0\right)N\left(0, \sigma^2\right)\) are added to the real GTEx data.

mat = read.csv("../data/liver.csv")

The setting: \(\pi_0 = 0.5\), \(\sigma^2 = 9\)

N = 200
nsamp = 10
ngene = 1e4
pi0 = 0.5
sd = 3
set.seed(777)
system.time(gdash.comp <- N_simulations(N, mat, nsamp, ngene, pi0, sd))
     user    system   elapsed 
12622.459  1340.169 49686.171 

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