<!DOCTYPE html> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="pandoc" /> <meta name="author" content="Lei Sun" /> <meta name="date" content="2017-05-27" /> <title>Simulation with Realistic Standard Error</title> <script src="site_libs/jquery-1.11.3/jquery.min.js"></script> <meta name="viewport" content="width=device-width, initial-scale=1" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script> <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script> <script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script> <link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" /> <script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script> <script src="site_libs/navigation-1.1/tabsets.js"></script> <link href="site_libs/highlightjs-1.1/textmate.css" rel="stylesheet" /> <script src="site_libs/highlightjs-1.1/highlight.js"></script> <link href="site_libs/font-awesome-4.5.0/css/font-awesome.min.css" rel="stylesheet" /> <style type="text/css">code{white-space: pre;}</style> <style type="text/css"> pre:not([class]) { background-color: white; } </style> <script type="text/javascript"> if (window.hljs && document.readyState && document.readyState === "complete") { window.setTimeout(function() { hljs.initHighlighting(); }, 0); } </script> <style type="text/css"> h1 { font-size: 34px; } h1.title { font-size: 38px; } h2 { font-size: 30px; } h3 { font-size: 24px; } h4 { font-size: 18px; } h5 { font-size: 16px; } h6 { font-size: 12px; } .table th:not([align]) { text-align: left; } </style> </head> <body> <style type = "text/css"> .main-container { max-width: 940px; margin-left: auto; margin-right: auto; } code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } img { max-width:100%; height: auto; } .tabbed-pane { padding-top: 12px; } button.code-folding-btn:focus { outline: none; } </style> <style type="text/css"> /* padding for bootstrap navbar */ body { padding-top: 51px; padding-bottom: 40px; } /* offset scroll position for anchor links (for fixed navbar) */ .section h1 { padding-top: 56px; margin-top: -56px; } .section h2 { padding-top: 56px; margin-top: -56px; } .section h3 { padding-top: 56px; margin-top: -56px; } .section h4 { padding-top: 56px; margin-top: -56px; } .section h5 { padding-top: 56px; margin-top: -56px; } .section h6 { padding-top: 56px; margin-top: -56px; } </style> <script> // manage active state of menu based on current page $(document).ready(function () { // active menu anchor href = window.location.pathname href = href.substr(href.lastIndexOf('/') + 1) if (href === "") href = "index.html"; var menuAnchor = $('a[href="' + href + '"]'); // mark it active menuAnchor.parent().addClass('active'); // if it's got a parent navbar menu mark it active as well menuAnchor.closest('li.dropdown').addClass('active'); }); </script> <div class="container-fluid main-container"> <!-- tabsets --> <script> $(document).ready(function () { window.buildTabsets("TOC"); }); </script> <!-- code folding --> <script> $(document).ready(function () { // move toc-ignore selectors from section div to header $('div.section.toc-ignore') .removeClass('toc-ignore') .children('h1,h2,h3,h4,h5').addClass('toc-ignore'); // establish options var options = { selectors: "h1,h2,h3", theme: "bootstrap3", context: '.toc-content', hashGenerator: function (text) { return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase(); }, ignoreSelector: ".toc-ignore", scrollTo: 0 }; options.showAndHide = true; options.smoothScroll = true; // tocify var toc = $("#TOC").tocify(options).data("toc-tocify"); }); </script> <style type="text/css"> #TOC { margin: 25px 0px 20px 0px; } @media (max-width: 768px) { #TOC { position: relative; width: 100%; } } .toc-content { padding-left: 30px; padding-right: 40px; } div.main-container { max-width: 1200px; } div.tocify { width: 20%; max-width: 260px; max-height: 85%; } @media (min-width: 768px) and (max-width: 991px) { div.tocify { width: 25%; } } @media (max-width: 767px) { div.tocify { width: 100%; max-width: none; } } .tocify ul, .tocify li { line-height: 20px; } .tocify-subheader .tocify-item { font-size: 0.90em; padding-left: 25px; text-indent: 0; } .tocify .list-group-item { border-radius: 0px; } </style> <!-- setup 3col/9col grid for toc_float and main content --> <div class="row-fluid"> <div class="col-xs-12 col-sm-4 col-md-3"> <div id="TOC" class="tocify"> </div> </div> <div class="toc-content col-xs-12 col-sm-8 col-md-9"> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a class="navbar-brand" href="index.html">truncash</a> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html">Home</a> </li> <li> <a href="about.html">About</a> </li> <li> <a href="license.html">License</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/LSun/truncash"> <span class="fa fa-github"></span> </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> <div class="fluid-row" id="header"> <h1 class="title toc-ignore">Simulation with Realistic Standard Error</h1> <h4 class="author"><em>Lei Sun</em></h4> <h4 class="date"><em>2017-05-27</em></h4> </div> <!-- The file analysis/chunks.R contains chunks that define default settings shared across the workflowr files. --> <!-- Update knitr chunk options --> <!-- Insert the date the file was last updated --> <p><strong>Last updated:</strong> 2017-06-01</p> <!-- Insert the code version (Git commit SHA1) if Git repository exists and R package git2r is installed --> <p><strong>Code version:</strong> a40ffff</p> <!-- Add your analysis here --> <pre class="r"><code>library(ashr) library(edgeR) library(limma) library(pROC)</code></pre> <pre class="r"><code>source("../code/gdash.R")</code></pre> <div id="read-in-data" class="section level2"> <h2>Read in data</h2> <pre class="r"><code>data = readRDS("../data/liver.rds") ngene = 1e4 data = top_gene_selection(ngene, data)$data</code></pre> </div> <div id="global-null" class="section level2"> <h2>Global Null</h2> <p><span class="math display">\[ g \equiv 0 \ . \]</span></p> <p><img src="figure/simulation_real_se.rmd/null plotting-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/simulation_real_se.rmd/null plotting-2.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/null%20average%20fdp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/null%20average%20fsp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="snr-0" class="section level2"> <h2>SNR = 0</h2> <p><span class="math display">\[ g = 0.6\delta_0 + 0.3N\left(0, \sigma^2\right) + 0.1N\left(0, \left(2.65\sigma\right)^2\right) \ . \]</span></p> <p><img src="figure/simulation_real_se.rmd/zero plotting-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/simulation_real_se.rmd/zero plotting-2.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/zero auc plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/zero%20average%20fdp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/zero%20average%20fsp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="snr-2" class="section level2"> <h2>SNR = 2</h2> <p><span class="math display">\[ g = 0.6\delta_0 + 0.3N\left(0, \sigma^2\right) + 0.1N\left(0, \left(3.58\sigma\right)^2\right) \ . \]</span></p> <p><img src="figure/simulation_real_se.rmd/small plotting-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/simulation_real_se.rmd/small plotting-2.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/small auc plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/small%20average%20fdp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/small%20average%20fsp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="snr-5" class="section level2"> <h2>SNR = 5</h2> <p><span class="math display">\[ g = 0.6\delta_0 + 0.3N\left(0, \left(2\sigma\right)^2\right) + 0.1N\left(0, \left(4.43\sigma\right)^2\right) \ . \]</span></p> <p><img src="figure/simulation_real_se.rmd/medium plotting-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/simulation_real_se.rmd/medium plotting-2.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/medium auc plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/medium%20average%20fdp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/medium%20average%20fsp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="snr-10" class="section level2"> <h2>SNR = 10</h2> <p><span class="math display">\[ g = 0.6\delta_0 + 0.3N\left(0, \left(3\sigma\right)^2\right) + 0.1N\left(0, \left(8.54\sigma\right)^2\right) \ . \]</span></p> <p><img src="figure/simulation_real_se.rmd/big plotting-1.png" width="672" style="display: block; margin: auto;" /><img src="figure/simulation_real_se.rmd/big plotting-2.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/big auc plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/big%20average%20fdp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> <p><img src="figure/simulation_real_se.rmd/big%20average%20fsp%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p> </div> <div id="session-information" class="section level2"> <h2>Session information</h2> <!-- Insert the session information into the document --> <pre class="r"><code>sessionInfo()</code></pre> <pre><code>R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.5 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] Rmosek_7.1.2 PolynomF_0.94 cvxr_0.0.0.9009 [4] REBayes_0.85 Matrix_1.2-10 SQUAREM_2016.10-1 [7] EQL_1.0-0 ttutils_1.0-1 pROC_1.9.1 [10] edgeR_3.14.0 limma_3.28.21 ashr_2.1-13 loaded via a namespace (and not attached): [1] Rcpp_0.12.10 knitr_1.16 magrittr_1.5 [4] MASS_7.3-47 doParallel_1.0.10 pscl_1.4.9 [7] lattice_0.20-35 foreach_1.4.3 plyr_1.8.4 [10] stringr_1.2.0 tools_3.3.3 parallel_3.3.3 [13] grid_3.3.3 git2r_0.18.0 htmltools_0.3.6 [16] iterators_1.0.8 yaml_2.1.14 rprojroot_1.2 [19] digest_0.6.12 codetools_0.2-15 evaluate_0.10 [22] rmarkdown_1.5 stringi_1.1.5 backports_1.0.5 [25] truncnorm_1.0-7 </code></pre> </div> <hr> <p> This <a href="http://rmarkdown.rstudio.com">R Markdown</a> site was created with <a href="https://github.com/jdblischak/workflowr">workflowr</a> </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'; // required: replace example with your forum shortname /* * * DON'T EDIT BELOW THIS LINE * * */ (function() { var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true; dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js'; (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq); })(); </script> <noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript> <a href="http://disqus.com" class="dsq-brlink">comments powered by <span class="logo-disqus">Disqus</span></a> --> </div> </div> </div> <script> // add bootstrap table styles to pandoc tables function bootstrapStylePandocTables() { $('tr.header').parent('thead').parent('table').addClass('table table-condensed'); } $(document).ready(function () { bootstrapStylePandocTables(); }); </script> <!-- dynamically load mathjax for compatibility with self-contained --> <script> (function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); </script> </body> </html>