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: 5b37742

    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_plots_fdp_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/

Untracked files:
    Untracked:  analysis/cash_plots_fdp_files/
    Untracked:  docs/cash_plots_fdp_files/
    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 fb76f41 LSun 2017-11-29 webpages
    rmd 8966bc7 LSun 2017-11-29 CASH on FDR
    html 5bc0531 LSun 2017-11-28 Build site.
    rmd 697ce5f LSun 2017-11-28 wflow_publish(c(“analysis/cash_fdr_1.rmd”, “analysis/cash_fdr_2.rmd”))
    html e52e79c LSun 2017-11-28 building sites
    html d2b3aeb LSun 2017-11-28 pages
    rmd 857728f LSun 2017-11-28 plotting
    html 92244e4 LSun 2017-11-28 Build site.
    rmd b8bcdda LSun 2017-11-28 wflow_publish(c(“analysis/index.Rmd”, “analysis/cash_fdr_1.rmd”,

Introduction

The model is

\[ \beta_j \sim g(\cdot) \ ;\\ \hat\beta_j = \beta_j + \hat s_j z_j \ ;\\ z_j \sim N(0, 1) \ , \] where \[ g = 0.5\delta_0 + 0.5N(0, \sigma_n^2) \ . \] We consider three scenarios for the noise \(z_j\): 1. Correlated noise, simulated from real data; 2. Independent noise; 3. Correlated noise, simulated from artificial data.

nsim <- 100
ngene <- 1000
pi0 <- 0.5
snr <- 1
FDR.nominal <- seq(0, 0.1, 0.001)[-1]

Correlated noise, real data

Expand here to see past versions of cor pihat0-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
5bc0531 LSun 2017-11-28
92244e4 LSun 2017-11-28

Expand here to see past versions of cor FDR plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
5bc0531 LSun 2017-11-28
92244e4 LSun 2017-11-28 
No id variables; using all as measure variables

Expand here to see past versions of cor FDR violin-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
fb76f41 LSun 2017-11-29
5bc0531 LSun 2017-11-28
d2b3aeb LSun 2017-11-28
92244e4 LSun 2017-11-28

Expand here to see past versions of cor FDR variability-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
fb76f41 LSun 2017-11-29
5bc0531 LSun 2017-11-28
d2b3aeb LSun 2017-11-28
92244e4 LSun 2017-11-28

Expand here to see past versions of cor FDR tail-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
5bc0531 LSun 2017-11-28
d2b3aeb LSun 2017-11-28
92244e4 LSun 2017-11-28

Expand here to see past versions of cor FDR tail-2.png:
Version Author Date
0f36d99 LSun 2017-12-21
5bc0531 LSun 2017-11-28
d2b3aeb LSun 2017-11-28
92244e4 LSun 2017-11-28

Independent noise

Expand here to see past versions of indep pihat0-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
fb76f41 LSun 2017-11-29
92244e4 LSun 2017-11-28

Expand here to see past versions of indep FDR plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
fb76f41 LSun 2017-11-29
92244e4 LSun 2017-11-28

Correlated noise, synthetic data

Expand here to see past versions of syn pihat0-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
fb76f41 LSun 2017-11-29
5bc0531 LSun 2017-11-28
92244e4 LSun 2017-11-28

Expand here to see past versions of syn FDR plotting-1.png:
Version Author Date
0f36d99 LSun 2017-12-21
fb76f41 LSun 2017-11-29
5bc0531 LSun 2017-11-28
92244e4 LSun 2017-11-28

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     

other attached packages:
 [1] edgeR_3.20.2      limma_3.34.4      ggplot2_2.2.1    
 [4] reshape2_1.4.3    ashr_2.2-2        Rmosek_8.0.69    
 [7] PolynomF_1.0-1    CVXR_0.95         REBayes_1.2      
[10] Matrix_1.2-12     SQUAREM_2017.10-1 EQL_1.0-0        
[13] ttutils_1.0-1    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16        locfit_1.5-9.1      lattice_0.20-35    
 [4] rprojroot_1.3-2     digest_0.6.15       foreach_1.4.4      
 [7] gmp_0.5-13.1        truncnorm_1.0-7     R6_2.2.2           
[10] plyr_1.8.4          backports_1.1.2     acepack_1.4.1      
[13] evaluate_0.10.1     pillar_1.0.1        rlang_0.1.6        
[16] lazyeval_0.2.1      pscl_1.5.2          data.table_1.10.4-3
[19] rstudioapi_0.7      whisker_0.3-2       R.utils_2.6.0      
[22] R.oo_1.21.0         rpart_4.1-11        checkmate_1.8.5    
[25] rmarkdown_1.9       labeling_0.3        splines_3.4.3      
[28] stringr_1.3.0       foreign_0.8-69      htmlwidgets_0.9    
[31] bit_1.1-12          munsell_0.4.3       compiler_3.4.3     
[34] base64enc_0.1-3     htmltools_0.3.6     nnet_7.3-12        
[37] htmlTable_1.11.1    tibble_1.4.1        gridExtra_2.3      
[40] workflowr_1.0.1     Hmisc_4.1-0         codetools_0.2-15   
[43] MASS_7.3-47         R.methodsS3_1.7.1   grid_3.4.3         
[46] gtable_0.2.0        git2r_0.21.0        magrittr_1.5       
[49] scales_0.5.0        stringi_1.1.6       Rmpfr_0.6-1        
[52] doParallel_1.0.11   latticeExtra_0.6-28 Formula_1.2-2      
[55] RColorBrewer_1.1-2  iterators_1.0.9     tools_3.4.3        
[58] bit64_0.9-7         parallel_3.4.3      survival_2.41-3    
[61] yaml_2.1.18         colorspace_1.3-2    cluster_2.0.6      
[64] scs_1.1-1           ECOSolveR_0.4       knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.0.1