Last updated: 2018-05-15

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Expand here to see past versions:
    File Version Author Date Message
    html e05bc83 LSun 2018-05-12 Update to 1.0
    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 ce86d60 LSun 2017-07-03 Build site.
    rmd 84a84ca LSun 2017-04-23 diagnostic plots
    html 84a84ca LSun 2017-04-23 diagnostic plots

We take a look at those data sets where BH gives no (false) discoveries at FDR \(\alpha = 0.05\), and at the same time ASH estimates \(\hat\pi_0 \leq 0.1\). For each data set, \(z\) scores, \(p\) values, and diagnostic \(\hat F_j\) are plotted.

library(ashr)
z = read.table("../output/z_null_liver_777.txt")
p = read.table("../output/p_null_liver_777.txt")
pihat0 = as.numeric(unlist(read.table("../output/pihat0_z_null_liver_777.txt")))
fd.bh = as.numeric(unlist(read.table("../output/fd.bh.0.05_null_liver_777.txt")))
N0. 1 : Data Set 33 ; Number of False Discoveries: 0 ; pihat0 = 0.01048871

N0. 2 : Data Set 537 ; Number of False Discoveries: 0 ; pihat0 = 0.01174394

N0. 3 : Data Set 693 ; Number of False Discoveries: 0 ; pihat0 = 0.01296388

N0. 4 : Data Set 885 ; Number of False Discoveries: 0 ; pihat0 = 0.01285109

N0. 5 : Data Set 705 ; Number of False Discoveries: 0 ; pihat0 = 0.03966321

N0. 6 : Data Set 40 ; Number of False Discoveries: 0 ; pihat0 = 0.04225311

N0. 7 : Data Set 338 ; Number of False Discoveries: 0 ; pihat0 = 0.01832042

N0. 8 : Data Set 379 ; Number of False Discoveries: 0 ; pihat0 = 0.03824364

N0. 9 : Data Set 649 ; Number of False Discoveries: 0 ; pihat0 = 0.02077128

N0. 10 : Data Set 627 ; Number of False Discoveries: 0 ; pihat0 = 0.02034137

N0. 11 : Data Set 133 ; Number of False Discoveries: 0 ; pihat0 = 0.04729238

N0. 12 : Data Set 915 ; Number of False Discoveries: 0 ; pihat0 = 0.03371413

N0. 13 : Data Set 999 ; Number of False Discoveries: 0 ; pihat0 = 0.04802764

N0. 14 : Data Set 182 ; Number of False Discoveries: 0 ; pihat0 = 0.04835373

N0. 15 : Data Set 511 ; Number of False Discoveries: 0 ; pihat0 = 0.04832825

N0. 16 : Data Set 937 ; Number of False Discoveries: 0 ; pihat0 = 0.04736585

N0. 17 : Data Set 495 ; Number of False Discoveries: 0 ; pihat0 = 0.04841265

N0. 18 : Data Set 41 ; Number of False Discoveries: 0 ; pihat0 = 0.03013827

N0. 19 : Data Set 3 ; Number of False Discoveries: 0 ; pihat0 = 0.04912382

N0. 20 : Data Set 907 ; Number of False Discoveries: 0 ; pihat0 = 0.03578098

N0. 21 : Data Set 809 ; Number of False Discoveries: 0 ; pihat0 = 0.03198968

N0. 22 : Data Set 404 ; Number of False Discoveries: 0 ; pihat0 = 0.01757131

N0. 23 : Data Set 800 ; Number of False Discoveries: 0 ; pihat0 = 0.0352261

N0. 24 : Data Set 562 ; Number of False Discoveries: 0 ; pihat0 = 0.05014307

N0. 25 : Data Set 893 ; Number of False Discoveries: 0 ; pihat0 = 0.0422105

N0. 26 : Data Set 780 ; Number of False Discoveries: 0 ; pihat0 = 0.05197813

N0. 27 : Data Set 538 ; Number of False Discoveries: 0 ; pihat0 = 0.04976013

N0. 28 : Data Set 324 ; Number of False Discoveries: 0 ; pihat0 = 0.04925775

N0. 29 : Data Set 176 ; Number of False Discoveries: 0 ; pihat0 = 0.03005686

N0. 30 : Data Set 972 ; Number of False Discoveries: 0 ; pihat0 = 0.06009152

N0. 31 : Data Set 644 ; Number of False Discoveries: 0 ; pihat0 = 0.06256917

N0. 32 : Data Set 977 ; Number of False Discoveries: 0 ; pihat0 = 0.06351771

N0. 33 : Data Set 467 ; Number of False Discoveries: 0 ; pihat0 = 0.0513426

N0. 34 : Data Set 857 ; Number of False Discoveries: 0 ; pihat0 = 0.07138568

N0. 35 : Data Set 976 ; Number of False Discoveries: 0 ; pihat0 = 0.06447058

N0. 36 : Data Set 968 ; Number of False Discoveries: 0 ; pihat0 = 0.05946434

N0. 37 : Data Set 942 ; Number of False Discoveries: 0 ; pihat0 = 0.02694257

N0. 38 : Data Set 402 ; Number of False Discoveries: 0 ; pihat0 = 0.07096583

N0. 39 : Data Set 341 ; Number of False Discoveries: 0 ; pihat0 = 0.04295436

N0. 40 : Data Set 411 ; Number of False Discoveries: 0 ; pihat0 = 0.05617472

N0. 41 : Data Set 484 ; Number of False Discoveries: 0 ; pihat0 = 0.03296313

N0. 42 : Data Set 476 ; Number of False Discoveries: 0 ; pihat0 = 0.06738787

N0. 43 : Data Set 407 ; Number of False Discoveries: 0 ; pihat0 = 0.02274312

N0. 44 : Data Set 871 ; Number of False Discoveries: 0 ; pihat0 = 0.07502045

N0. 45 : Data Set 638 ; Number of False Discoveries: 0 ; pihat0 = 0.05038079

N0. 46 : Data Set 232 ; Number of False Discoveries: 0 ; pihat0 = 0.07981507

N0. 47 : Data Set 349 ; Number of False Discoveries: 0 ; pihat0 = 0.08685835

N0. 48 : Data Set 985 ; Number of False Discoveries: 0 ; pihat0 = 0.04389071

N0. 49 : Data Set 259 ; Number of False Discoveries: 0 ; pihat0 = 0.06952575

N0. 50 : Data Set 452 ; Number of False Discoveries: 0 ; pihat0 = 0.04829788

N0. 51 : Data Set 268 ; Number of False Discoveries: 0 ; pihat0 = 0.07180346

N0. 52 : Data Set 526 ; Number of False Discoveries: 0 ; pihat0 = 0.06426254

N0. 53 : Data Set 685 ; Number of False Discoveries: 0 ; pihat0 = 0.04238147

N0. 54 : Data Set 499 ; Number of False Discoveries: 0 ; pihat0 = 0.07477045

N0. 55 : Data Set 982 ; Number of False Discoveries: 0 ; pihat0 = 0.04228667

N0. 56 : Data Set 582 ; Number of False Discoveries: 0 ; pihat0 = 0.08703327

N0. 57 : Data Set 953 ; Number of False Discoveries: 0 ; pihat0 = 0.06148864

N0. 58 : Data Set 811 ; Number of False Discoveries: 0 ; pihat0 = 0.06374408

N0. 59 : Data Set 231 ; Number of False Discoveries: 0 ; pihat0 = 0.1099259

N0. 60 : Data Set 781 ; Number of False Discoveries: 0 ; pihat0 = 0.04563832

N0. 61 : Data Set 853 ; Number of False Discoveries: 0 ; pihat0 = 0.07850494

N0. 62 : Data Set 868 ; Number of False Discoveries: 0 ; pihat0 = 0.1153411

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