Mercurial > repos > proteomisc > preprocess_dataset

diff preprocess_datasets/Affymetrix.Rmd @ 33:1367e5b24925 draft

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author proteomisc
date Mon, 11 Dec 2023 12:16:58 +0000
parents 3744b476edc9
children 0aa849aec11e
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line diff
--- a/preprocess_datasets/Affymetrix.Rmd	Mon Dec 11 11:58:11 2023 +0000
+++ b/preprocess_datasets/Affymetrix.Rmd	Mon Dec 11 12:16:58 2023 +0000
@@ -1,91 +1,57 @@
-<html>
+<!DOCTYPE html>
+<html lang="en">
 <head>
-<meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
-<title>Preprocessing Plots Before and After</title>
-<style>
-div.tpR {
-  font-family: serif;
-  color: #000000;
-  background-color: #fff;
-}
-div.tpR h1 {
- font-family: sans-serif;
- color: #000;
- border-style: solid;
- background-color: #ddf;
- border-color: #88f;
- border-width: 1px;
- padding-left: 0.5em;
-}
-
-div.tpR h2 {
- font-family: sans-serif;
- color: #000;
- border-style: solid;
- border-color: #8f8;
- background-color: #dfd;
- border-width: 1px;
- padding-left: 0.5em;
-}
-
-div.tpR h3 {
- font-family: sans-serif;
- color: #000;
- border-style: solid;
- background-color: #fdd;
- border-color: #f88;
- border-width: 1px;
- padding-left: 0.5em;
-}
-</style>
+    <meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
+    <title>Preprocessing Plots Before and After</title>
 </head>
 <body>
 <div class="tpR">
-<h1>Preprocessing</h1>
-<p>
-Preprocessing of an `r datasetsource` DataSet, issued from 
-`r technology` 
-technology.  
-</p>
-<h2>Used methods for each step</h2>
+    <h1>Preprocessing</h1>
+    <p>
+        Preprocessing of an `r datasetsource` DataSet, issued from
+        `r technology`
+        technology.
+    </p>
+    <h2>Used methods for each step</h2>
 
-<h3>Background correction methods</h3>
-<pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
-<h3>Normalization methods</h3>
-<pre>method : `r listArguments[["normalization_method"]]`</pre>
-<h3>Summarization methods</h3>
-<pre>method : `r listArguments[["summary_method"]]`</pre>
-<h2>Boxplots</h2>
-<h3>Before NM</h3>
-<p>
-<br>
-<img src="boxplot_before_NM.png" width="100%" height="auto">
-<br>
-</p>
-<h3>After NM</h3>
-<p>
-<br>
-<img src="boxplot_after_NM.png" width="100%" height="auto">
-<br>
-</p>
-<h2>MA plots</h2>
-<p>
-<br>
-<img src="MA_plot.png" width="100%" height="auto">
-<br>
-</p>
-<h2>Densities plot</h2>
-<h3>Before NM</h3>
-<p>
-<br>
-<img src="densities_plot_before_NM.png" width="100%" height="auto">
-<br>
-</p>
-<h3>After NM</h3>
-<p>
-<br>
-<img src="densities_plot_after_NM.png" width="100%" height="auto">
-<br>
-</p>
+    <h3>Background correction methods</h3>
+    <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
+    <h3>Normalization methods</h3>
+    <pre>method : `r listArguments[["normalization_method"]]`</pre>
+    <h3>Summarization methods</h3>
+    <pre>method : `r listArguments[["summary_method"]]`</pre>
+    <h2>Boxplots</h2>
+    <h3>Before NM</h3>
+    <p>
+        <br>
+        <img src="boxplot_before_NM.png" width="100%" height="auto" alt="">
+        <br>
+    </p>
+    <h3>After NM</h3>
+    <p>
+        <br>
+        <img src="boxplot_after_NM.png" width="100%" height="auto" alt="">
+        <br>
+    </p>
+    <h2>MA plots</h2>
+    <p>
+        <br>
+        <img src="MA_plot.png" width="100%" height="auto" alt="">
+        <br>
+    </p>
+    <h2>Densities plot</h2>
+    <h3>Before NM</h3>
+    <p>
+        <br>
+        <img src="densities_plot_before_NM.png" width="100%" height="auto" alt="">
+        <br>
+    </p>
+    <h3>After NM</h3>
+    <p>
+        <br>
+        <img src="densities_plot_after_NM.png" width="100%" height="auto" alt="">
+        <br>
+    </p>
+</div>
 </body>
-</html>
+</html>
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