Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Browse files

broken links in the Slides fixed

  • Loading branch information...
commit 55840f9c48ec21d41de691fa11bd40cde27b829b 1 parent 786eda5
@onertipaday authored
Showing with 44 additions and 46 deletions.
  1. +3 −3 Slides/Slides.Rmd
  2. +21 −23 Slides/Slides.html
  3. +20 −20 Slides/Slides.md
View
6 Slides/Slides.Rmd
@@ -283,7 +283,7 @@ Bioconductor [^4]
* To further scientific understanding by producing high-quality documentation and reproducible research.
* To train researchers on computational and statistical methods for the analysis of genomic data.
-[^3]: [Bioconductor web site](bioconductor.org)
+[^4]: [Bioconductor web site](bioconductor.org)
Why Bioconductor is the way to follow for Reproducible Research
===
@@ -339,8 +339,8 @@ Case Study - Conclusion
Slides and Example
===
These slides and the Case Study were performed using the package knitr for converting either the RMarkdown into Markdown (slides) or Sweave markup to pdf (case study), pandoc to generate the html5 from Markdown.
-The case study is available at [https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy](https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy).
-The slides are available at [https://github.com/onertipaday/ItalianBioRDay2012/Slides](https://github.com/onertipaday/ItalianBioRDay2012/Slides)
+The case study is available at [https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy](https://github.com/onertipaday/ItalianBioRDay2012/tree/master/CaseStudy).
+The slides are available at [https://github.com/onertipaday/ItalianBioRDay2012/Slides](https://github.com/onertipaday/ItalianBioRDay2012/tree/master/Slides)
and can be replicated from R by typing (package [knitr](http://yihui.name/knitr/) should be installed in your R distribution and [pandoc](http://johnmacfarlane.net/pandoc/) available on your system):
```{r Slides, eval=FALSE, echo=TRUE, tidy=TRUE}
View
44 Slides/Slides.html
@@ -192,13 +192,13 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<pre><code>&lt;&lt;hello sweave &gt;&gt;=
print(rnorm(50))
@</code></pre>
-<pre><code>## [1] 0.37455 0.26448 0.11821 0.25493 0.66274 1.22757 -1.83224 -1.41128
-## [9] 0.30672 0.79322 -1.17644 0.86704 0.53878 -0.27332 1.43887 -0.29149
-## [17] 0.78745 0.56054 -0.15015 0.63875 -1.77446 1.05768 2.04004 0.39984
-## [25] -0.75676 -0.95623 1.45970 1.40448 -0.59392 -0.39692 0.24093 -0.19675
-## [33] 1.16757 -0.17791 -0.69001 3.54292 0.77806 -0.38563 0.17216 0.84204
-## [41] 1.73025 0.45344 -0.19087 0.24172 -0.15962 0.03867 -2.04133 0.15311
-## [49] -1.05571 -0.32733</code></pre>
+<pre><code>## [1] -1.02809 0.58519 0.47856 -1.15948 0.35598 -0.19351 -1.13424 0.63789
+## [9] 1.69889 -1.11168 1.01274 -1.86981 -0.03253 -1.23849 0.65434 0.51970
+## [17] -0.17844 0.15562 -0.31640 0.73339 1.58082 0.28131 -0.49190 -0.53323
+## [25] -0.64260 0.06578 -1.07761 0.88227 -0.33908 -0.29489 0.65853 0.49415
+## [33] 0.91659 -0.20477 -0.33838 1.67765 -0.70644 -0.55799 -0.26238 -0.19877
+## [41] -0.49096 -1.33861 -0.39981 0.41306 0.01421 -0.53587 0.48340 2.28866
+## [49] -1.33952 -1.84252</code></pre>
<p>Run <em>Sweave</em> to produce Tex, and <em>Stangle</em> to extract the R code</p>
<pre><code>R CMD Sweave helloworld.Rnw
R CMD Stangle helloworld.Rnw
@@ -233,13 +233,13 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<blockquote>
<p>```{r hello_rmarkdown}<br />print(rnorm(50))<br />```</p>
</blockquote>
-<pre><code>## [1] 1.16065 0.37597 -0.80841 0.42764 0.25866 0.33264 -1.74833 -0.98599
-## [9] 1.23975 0.21318 1.16210 -1.94610 0.97251 0.30657 1.90265 0.13068
-## [17] 0.08775 -1.99787 -1.20159 1.53788 0.37576 -0.49226 -0.91396 1.02579
-## [25] -0.48610 1.28597 0.36403 -0.35805 -1.18346 0.90558 0.65471 1.33404
-## [33] -0.18939 0.30535 -1.46421 0.12731 0.82822 -0.16294 -0.61968 0.15297
-## [41] 0.10214 -0.07084 -1.95884 1.91617 -0.46115 -1.99758 0.15627 0.67087
-## [49] 0.28523 -1.97344</code></pre>
+<pre><code>## [1] 0.47135 0.33137 1.12405 -1.93464 0.49882 -0.40663 1.70079 1.95296
+## [9] 0.28356 0.46559 -1.60801 -0.51435 -1.14396 1.38524 1.41066 -0.51923
+## [17] 0.01728 -1.15363 1.05206 -1.38199 -0.47508 1.18964 -0.35563 -0.41657
+## [25] -0.70746 1.41704 -0.65796 -0.11216 0.67053 -0.11592 0.49551 -0.17050
+## [33] 0.36816 0.06961 -0.32033 -0.60880 -0.72954 -0.60811 -0.02811 1.25004
+## [41] -0.35045 1.64920 1.58694 -0.05738 0.68935 -0.03911 0.94360 1.18036
+## [49] 0.45375 -0.04956</code></pre>
<ul class="incremental">
<li>It requires the <em>knitr</em> package for producing a markdown document which can be converted into <em>html, pdf, etc</em>.</li>
</ul>
@@ -306,9 +306,6 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<h1><a href="http://subversion.apache.org/">Apache Subversion</a></h1>
<p>“Enterprise-class centralized version control for the masses”</p>
<p>Subversion exists to be universally recognized and adopted as an open-source, centralized version control system characterized by its reliability as a safe haven for valuable data; the simplicity of its model and usage; and its ability to support the needs of a wide variety of users and projects, from individuals to large-scale enterprise operations.</p>
-<div class="figure">
-<img src="images/r-forge.png" /><p class="caption"></p>
-</div>
</div>
<div class="section slide level1" id="svn-hello-world">
<h1>svn “Hello World”</h1>
@@ -357,8 +354,8 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<h1>R and Bioconductor</h1>
<img src="figure/wordcloud.png" width="400px" height="400px" alt="" title="" />
</div>
-<div class="section slide level1" id="bioconductor">
-<h1>Bioconductor</h1>
+<div class="section slide level1" id="bioconductor-bioconductor-web-site">
+<h1>Bioconductor <sup><a href="#fn4" class="footnoteRef" id="fnref4">4</a></sup></h1>
<ul class="incremental">
<li>Bioconductor is an open source project to provide tools for the analysis and comprehension of high-throughput genomic data, based primarily on the R programming language.</li>
<li>The broad goals of the Bioconductor project are:
@@ -398,7 +395,7 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<li>Use a Version Control System for recording your source code changes</li>
<li>Create pipelines producing documents including both the analysis and the working code (<em>Literate Programming</em>)</li>
<li>Use Bioconductor and include the version of your packages and the session info in the document</li>
-<li>One last thing:
+<li>One more thing:
<ul class="incremental">
<li>The Bioconductor team has developed an Amazon Machine Image (<a href="http://www.bioconductor.org/help/bioconductor-cloud-ami/">AMI</a>) that is optimized for running Bioconductor in the Amazon Elastic Compute Cloud (or EC2) for sequencing tasks.</li>
<li>storing data, code, packages in a frozen Virtual Machine allows the complete reproducibility of your analysis and make easy to share the results</li>
@@ -420,7 +417,7 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<div class="section slide level1" id="case-study---conclusion">
<h1>Case Study - Conclusion</h1>
<ul class="incremental">
-<li>We selected to replicate the Class Prediction analysis depicted in the manuscript: The authors taking advantage of the nearest shrunken centroid method (PAM) <sup><a href="#fn4" class="footnoteRef" id="fnref4">4</a></sup> wanted to identify the gene expressions patterns (signatures) of the contrasts adenoma vs normal biopsy samples and colorectal cancer (CRC) vs normal biopsy samples.</li>
+<li>We selected to replicate the Class Prediction analysis depicted in the manuscript: The authors taking advantage of the nearest shrunken centroid method (PAM) <sup><a href="#fn5" class="footnoteRef" id="fnref5">5</a></sup> wanted to identify the gene expressions patterns (signatures) of the contrasts adenoma vs normal biopsy samples and colorectal cancer (CRC) vs normal biopsy samples.</li>
<li>The results of our analysis were different from the manuscript (they matched them only partially).</li>
<li>Why this analysis can be replicated exactly?
<ul class="incremental">
@@ -432,7 +429,7 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
</div>
<div class="section slide level1" id="slides-and-example">
<h1>Slides and Example</h1>
-<p>These slides and the Case Study were performed using the package knitr for converting either the RMarkdown into Markdown (slides) or Sweave markup to pdf (case study), pandoc to generate the html5 from Markdown. The case study is available at <a href="https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy">https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy</a>. The slides are available at <a href="https://github.com/onertipaday/ItalianBioRDay2012/Slides">https://github.com/onertipaday/ItalianBioRDay2012/Slides</a><br />and can be replicated from R by typing (package <a href="http://yihui.name/knitr/">knitr</a> should be installed in your R distribution and <a href="http://johnmacfarlane.net/pandoc/">pandoc</a> available on your system):</p>
+<p>These slides and the Case Study were performed using the package knitr for converting either the RMarkdown into Markdown (slides) or Sweave markup to pdf (case study), pandoc to generate the html5 from Markdown. The case study is available at <a href="https://github.com/onertipaday/ItalianBioRDay2012/tree/master/CaseStudy">https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy</a>. The slides are available at <a href="https://github.com/onertipaday/ItalianBioRDay2012/tree/master/Slides">https://github.com/onertipaday/ItalianBioRDay2012/Slides</a><br />and can be replicated from R by typing (package <a href="http://yihui.name/knitr/">knitr</a> should be installed in your R distribution and <a href="http://johnmacfarlane.net/pandoc/">pandoc</a> available on your system):</p>
<pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(<span class="st">&quot;knitr&quot;</span>)
<span class="kw">knit</span>(<span class="st">&quot;Slides.Rmd&quot;</span>)
<span class="kw">system</span>(<span class="st">&quot;pandoc -s -S -i -t slidy --mathjax Slides.md -o Slides.html&quot;</span>)
@@ -474,7 +471,8 @@ <h1 class="title">Reproducible Research in High-Throughput Biology: A Case Study
<li id="fn1"><p><a href="http://blog.revolutionanalytics.com/2011/07/nyt-on-the-importance-of-reproducible-research.html">NYT on the importance of reproducible research</a>.<a href="#fnref1">↩</a></p></li>
<li id="fn2"><p><a href="http://en.wikipedia.org/wiki/Anil_Potti">Anil Potti page on Wikipedia</a>.<a href="#fnref2">↩</a></p></li>
<li id="fn3"><p>quotes from <a href="http://faculty.mdanderson.org/Keith_Baggerly/">Keith Baggerly</a>.<a href="#fnref3">↩</a></p></li>
-<li id="fn4"><p>T. Hastie, R. Tibshirani, Balasubramanian Narasimhan and Gil Chu (2011).<br /><a href="http://CRAN.R-project.org/package=pamr">pamr</a>: Pam: prediction analysis for microarrays. R package version 1.54.<a href="#fnref4">↩</a></p></li>
+<li id="fn4"><p><a href="bioconductor.org">Bioconductor web site</a><a href="#fnref4">↩</a></p></li>
+<li id="fn5"><p>T. Hastie, R. Tibshirani, Balasubramanian Narasimhan and Gil Chu (2011).<br /><a href="http://CRAN.R-project.org/package=pamr">pamr</a>: Pam: prediction analysis for microarrays. R package version 1.54.<a href="#fnref5">↩</a></p></li>
</ol>
</div>
</body>
View
40 Slides/Slides.md
@@ -142,13 +142,13 @@ print(rnorm(50))
```
-## [1] 0.37455 0.26448 0.11821 0.25493 0.66274 1.22757 -1.83224 -1.41128
-## [9] 0.30672 0.79322 -1.17644 0.86704 0.53878 -0.27332 1.43887 -0.29149
-## [17] 0.78745 0.56054 -0.15015 0.63875 -1.77446 1.05768 2.04004 0.39984
-## [25] -0.75676 -0.95623 1.45970 1.40448 -0.59392 -0.39692 0.24093 -0.19675
-## [33] 1.16757 -0.17791 -0.69001 3.54292 0.77806 -0.38563 0.17216 0.84204
-## [41] 1.73025 0.45344 -0.19087 0.24172 -0.15962 0.03867 -2.04133 0.15311
-## [49] -1.05571 -0.32733
+## [1] -1.02809 0.58519 0.47856 -1.15948 0.35598 -0.19351 -1.13424 0.63789
+## [9] 1.69889 -1.11168 1.01274 -1.86981 -0.03253 -1.23849 0.65434 0.51970
+## [17] -0.17844 0.15562 -0.31640 0.73339 1.58082 0.28131 -0.49190 -0.53323
+## [25] -0.64260 0.06578 -1.07761 0.88227 -0.33908 -0.29489 0.65853 0.49415
+## [33] 0.91659 -0.20477 -0.33838 1.67765 -0.70644 -0.55799 -0.26238 -0.19877
+## [41] -0.49096 -1.33861 -0.39981 0.41306 0.01421 -0.53587 0.48340 2.28866
+## [49] -1.33952 -1.84252
```
@@ -185,13 +185,13 @@ It allows the insertion of R chunks in a markdown file as well as Sweave allows
```
-## [1] 1.16065 0.37597 -0.80841 0.42764 0.25866 0.33264 -1.74833 -0.98599
-## [9] 1.23975 0.21318 1.16210 -1.94610 0.97251 0.30657 1.90265 0.13068
-## [17] 0.08775 -1.99787 -1.20159 1.53788 0.37576 -0.49226 -0.91396 1.02579
-## [25] -0.48610 1.28597 0.36403 -0.35805 -1.18346 0.90558 0.65471 1.33404
-## [33] -0.18939 0.30535 -1.46421 0.12731 0.82822 -0.16294 -0.61968 0.15297
-## [41] 0.10214 -0.07084 -1.95884 1.91617 -0.46115 -1.99758 0.15627 0.67087
-## [49] 0.28523 -1.97344
+## [1] 0.47135 0.33137 1.12405 -1.93464 0.49882 -0.40663 1.70079 1.95296
+## [9] 0.28356 0.46559 -1.60801 -0.51435 -1.14396 1.38524 1.41066 -0.51923
+## [17] 0.01728 -1.15363 1.05206 -1.38199 -0.47508 1.18964 -0.35563 -0.41657
+## [25] -0.70746 1.41704 -0.65796 -0.11216 0.67053 -0.11592 0.49551 -0.17050
+## [33] 0.36816 0.06961 -0.32033 -0.60880 -0.72954 -0.60811 -0.02811 1.25004
+## [41] -0.35045 1.64920 1.58694 -0.05738 0.68935 -0.03911 0.94360 1.18036
+## [49] 0.45375 -0.04956
```
* It requires the _knitr_ package for producing a markdown document which can be converted into _html, pdf, etc_.
@@ -244,8 +244,6 @@ Versioning and Version Control Systems
Subversion exists to be universally recognized and adopted as an open-source, centralized version control system characterized by its reliability as a safe haven for valuable data; the simplicity of its model and usage; and its ability to support the needs of a wide variety of users and projects, from individuals to large-scale enterprise operations.
-![](images/r-forge.png)
-
svn "Hello World"
===
svnadmin create SVNrep
@@ -287,7 +285,7 @@ R and Bioconductor
<img src="figure/wordcloud.png" width="400px" height="400px" alt="" title="" />
-Bioconductor
+Bioconductor [^4]
===
* Bioconductor is an open source project to provide tools for the analysis and comprehension of high-throughput genomic data, based primarily on the R programming language.
* The broad goals of the Bioconductor project are:
@@ -297,6 +295,8 @@ Bioconductor
* To further scientific understanding by producing high-quality documentation and reproducible research.
* To train researchers on computational and statistical methods for the analysis of genomic data.
+[^4]: [Bioconductor web site](bioconductor.org)
+
Why Bioconductor is the way to follow for Reproducible Research
===
* Same programming environment with tools operating and cooperating between them in coherent ways
@@ -318,7 +318,7 @@ Summary
* Use a Version Control System for recording your source code changes
* Create pipelines producing documents including both the analysis and the working code (_Literate Programming_)
* Use Bioconductor and include the version of your packages and the session info in the document
-* One last thing:
+* One more thing:
* The Bioconductor team has developed an Amazon Machine Image ([AMI](http://www.bioconductor.org/help/bioconductor-cloud-ami/)) that is optimized for running Bioconductor in the Amazon Elastic Compute Cloud (or EC2) for sequencing tasks.
* storing data, code, packages in a frozen Virtual Machine allows the complete reproducibility of your analysis and make easy to share the results
@@ -351,8 +351,8 @@ Case Study - Conclusion
Slides and Example
===
These slides and the Case Study were performed using the package knitr for converting either the RMarkdown into Markdown (slides) or Sweave markup to pdf (case study), pandoc to generate the html5 from Markdown.
-The case study is available at [https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy](https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy).
-The slides are available at [https://github.com/onertipaday/ItalianBioRDay2012/Slides](https://github.com/onertipaday/ItalianBioRDay2012/Slides)
+The case study is available at [https://github.com/onertipaday/ItalianBioRDay2012/CaseStudy](https://github.com/onertipaday/ItalianBioRDay2012/tree/master/CaseStudy).
+The slides are available at [https://github.com/onertipaday/ItalianBioRDay2012/Slides](https://github.com/onertipaday/ItalianBioRDay2012/tree/master/Slides)
and can be replicated from R by typing (package [knitr](http://yihui.name/knitr/) should be installed in your R distribution and [pandoc](http://johnmacfarlane.net/pandoc/) available on your system):

0 comments on commit 55840f9

Please sign in to comment.
Something went wrong with that request. Please try again.