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<title>CASH on FDR, 2</title>

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<h1 class="title toc-ignore"><code>CASH</code> on FDR, 2</h1>
<h4 class="author"><em>Lei Sun</em></h4>
<h4 class="date"><em>2017-11-26</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> 2017-12-21</p>
<!-- Insert the code version (Git commit SHA1) if Git repository exists and R
 package git2r is installed -->
<p><strong>Code version:</strong> 6e42447</p>
<!-- Add your analysis here -->
<section id="introduction" class="level2">
<h2>Introduction</h2>
<p><span class="math display">\[
g = 0.5\delta_0 + 0.5N(0, (2\sigma_n)^2)
\]</span></p>
</section>
<section id="correlated-noise-real-data" class="level2">
<h2>Correlated noise, real data</h2>
<pre><code>Warning: Computation failed in `stat_summary()`:
Hmisc package required for this function</code></pre>
<p><img src="figure/cash_fdr_2.rmd/cor%20pihat0-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_fdr_2.rmd/cor%20FDR%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p>
<pre><code>No id variables; using all as measure variables</code></pre>
<pre><code>Warning: Computation failed in `stat_summary()`:
object &#39;mean_sdp&#39; of mode &#39;function&#39; was not found</code></pre>
<p><img src="figure/cash_fdr_2.rmd/cor%20FDR%20violin-1.png" width="672" style="display: block; margin: auto;" /></p>
<pre><code>Warning: Computation failed in `stat_summary()`:
object &#39;mean_sdp&#39; of mode &#39;function&#39; was not found

Warning: Computation failed in `stat_summary()`:
object &#39;mean_sdp&#39; of mode &#39;function&#39; was not found

Warning: Computation failed in `stat_summary()`:
object &#39;mean_sdp&#39; of mode &#39;function&#39; was not found</code></pre>
<p><img src="figure/cash_fdr_2.rmd/cor%20FDR%20variability-1.png" width="960" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_fdr_2.rmd/cor%20FDR%20tail-1.png" width="960" style="display: block; margin: auto;" /><img src="figure/cash_fdr_2.rmd/cor%20FDR%20tail-2.png" width="960" style="display: block; margin: auto;" /></p>
</section>
<section id="independent-noise" class="level2">
<h2>Independent noise</h2>
<pre><code>Warning: Computation failed in `stat_summary()`:
Hmisc package required for this function</code></pre>
<p><img src="figure/cash_fdr_2.rmd/indep%20pihat0-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_fdr_2.rmd/indep%20FDR%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p>
</section>
<section id="correlated-noise-synthetic-data" class="level2">
<h2>Correlated noise, synthetic data</h2>
<pre><code>Warning: Computation failed in `stat_summary()`:
Hmisc package required for this function</code></pre>
<p><img src="figure/cash_fdr_2.rmd/syn%20pihat0-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><img src="figure/cash_fdr_2.rmd/syn%20FDR%20plotting-1.png" width="672" style="display: block; margin: auto;" /></p>
</section>
<section id="session-information" class="level2">
<h2>Session information</h2>
<!-- Insert the session information into the document -->
<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 10.13.2

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_0.94-4       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] gmp_0.5-13.1      Rcpp_0.12.14      plyr_1.8.4       
 [4] compiler_3.4.3    git2r_0.20.0      R.methodsS3_1.7.1
 [7] R.utils_2.6.0     iterators_1.0.9   tools_3.4.3      
[10] digest_0.6.13     bit_1.1-12        tibble_1.3.4     
[13] gtable_0.2.0      evaluate_0.10.1   lattice_0.20-35  
[16] rlang_0.1.4       foreach_1.4.4     yaml_2.1.16      
[19] parallel_3.4.3    Rmpfr_0.6-1       ECOSolveR_0.3-2  
[22] stringr_1.2.0     knitr_1.17        locfit_1.5-9.1   
[25] rprojroot_1.3-1   bit64_0.9-7       grid_3.4.3       
[28] R6_2.2.2          rmarkdown_1.8     magrittr_1.5     
[31] scales_0.5.0      MASS_7.3-47       backports_1.1.2  
[34] codetools_0.2-15  htmltools_0.3.6   scs_1.1-1        
[37] colorspace_1.3-2  labeling_0.3      stringi_1.1.6    
[40] lazyeval_0.2.1    munsell_0.4.3     doParallel_1.0.11
[43] pscl_1.5.2        truncnorm_1.0-7   R.oo_1.21.0      </code></pre>
</section>

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