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} </style> <div class="fluid-row" id="header"> <h1 class="title toc-ignore">Diagnostic Plot for <code>ASH</code></h1> <h4 class="author"><em>Lei Sun</em></h4> <h4 class="date"><em>2017-05-05</em></h4> </div> <p><strong>Last updated:</strong> 2018-05-12</p> <strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small> <ul> <li> <details> <p><summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p> <p>Great! 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Below is the status of the Git repository when the results were generated: <pre><code> 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 </code></pre> 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. </details> </li> </ul> <details> <summary> <small><strong>Expand here to see past versions:</strong></small> </summary> <ul> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> File </th> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> <th style="text-align:left;"> Message </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> rmd </td> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/cc0ab8379469bc3726f1508cd81e4ecd6fef1b1a/analysis/diagnostic_ash.rmd" target="_blank">cc0ab83</a> </td> <td style="text-align:left;"> Lei Sun </td> <td style="text-align:left;"> 2018-05-11 </td> <td style="text-align:left;"> update </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/0f36d998db26444c5dd01502ea1af7fbd1129b22/docs/diagnostic_ash.html" target="_blank">0f36d99</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-12-21 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/853a484bfacf347e109f6c8fb3ffaab5f4d6cc02/docs/diagnostic_ash.html" target="_blank">853a484</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-11-07 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/043bf895b4a909cf842ddfa19a7187908f608fa8/docs/diagnostic_ash.html" target="_blank">043bf89</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-11-05 </td> <td style="text-align:left;"> transfer </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/27bcaf9682ee32f9f548c6e5516f0c8ef684663c/docs/diagnostic_ash.html" target="_blank">27bcaf9</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-05-08 </td> <td style="text-align:left;"> writeups </td> </tr> <tr> <td style="text-align:left;"> rmd </td> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/6bac69e4ab027a161595872353a444b19769c794/analysis/diagnostic_ash.rmd" target="_blank">6bac69e</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-05-08 </td> <td style="text-align:left;"> writeups </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/LSun/truncash/5550dff8e7611994b0edd753f6a5244a36202bfc/docs/diagnostic_ash.html" target="_blank">5550dff</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-05-05 </td> <td style="text-align:left;"> diagnostic </td> </tr> <tr> <td style="text-align:left;"> rmd </td> <td style="text-align:left;"> <a href="https://github.com/LSun/truncash/blob/87514940674fda75ae234d89a9799aac4860abf5/analysis/diagnostic_ash.rmd" target="_blank">8751494</a> </td> <td style="text-align:left;"> LSun </td> <td style="text-align:left;"> 2017-05-05 </td> <td style="text-align:left;"> diagnostic </td> </tr> </tbody> </table> </ul> </details> <hr /> <div id="introduction" class="section level2"> <h2>Introduction</h2> <p>Based on discussion with Matthew on several ideas to improve the diagnostic plot for <code>ASH</code>, this file documents the latest version of <code>plot_diagnostic</code> function in <code>ashr</code>.</p> <pre class="r"><code>library(ashr)</code></pre> </div> <div id="alpha-0.01-rather-than-0.05." class="section level2"> <h2><span class="math inline">\(\alpha = 0.01\)</span> rather than <span class="math inline">\(0.05\)</span>.</h2> <p>The idea is to “reduce the number of crossings some, but still give a good idea of what is expected without being too conservative.”</p> <p><img src="figure/diagnostic_ash.rmd/0.01-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-2.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-3.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-4.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-5.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-6.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-7.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-8.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-9.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/0.01-10.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="other-ideas" class="section level2"> <h2>Other ideas</h2> <p>All have been put into the <code>ashr::plot_diagnostic</code> function.</p> </div> <div id="illustration" class="section level2"> <h2>Illustration</h2> <p><img src="figure/diagnostic_ash.rmd/unnamed-chunk-3-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/diagnostic_ash.rmd/unnamed-chunk-3-2.png" width="672" style="display: block; margin: auto;" /></p> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/diagnostic_ash.rmd/unnamed-chunk-3-3.png" width="672" style="display: block; margin: auto;" /></p> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/diagnostic_ash.rmd/unnamed-chunk-3-4.png" width="672" style="display: block; margin: auto;" /></p> <pre><code>Press [enter] to see next plot</code></pre> <p><img src="figure/diagnostic_ash.rmd/unnamed-chunk-3-5.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="session-information" class="section level2"> <h2>Session information</h2> <pre class="r"><code>sessionInfo()</code></pre> <pre><code>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 </code></pre> </div> <hr> <p> </p> <hr> <!-- To enable disqus, uncomment the section below and provide your disqus_shortname --> <!-- disqus <div id="disqus_thread"></div> <script type="text/javascript"> /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */ var disqus_shortname = 'rmarkdown'; 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