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comparison 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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32:3744b476edc9 33:1367e5b24925
1 <html> 1 <!DOCTYPE html>
2 <html lang="en">
2 <head> 3 <head>
3 <meta http-equiv="Content-Type" content="text/html; charset=windows-1252"> 4 <meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
4 <title>Preprocessing Plots Before and After</title> 5 <title>Preprocessing Plots Before and After</title>
5 <style>
6 div.tpR {
7 font-family: serif;
8 color: #000000;
9 background-color: #fff;
10 }
11 div.tpR h1 {
12 font-family: sans-serif;
13 color: #000;
14 border-style: solid;
15 background-color: #ddf;
16 border-color: #88f;
17 border-width: 1px;
18 padding-left: 0.5em;
19 }
20
21 div.tpR h2 {
22 font-family: sans-serif;
23 color: #000;
24 border-style: solid;
25 border-color: #8f8;
26 background-color: #dfd;
27 border-width: 1px;
28 padding-left: 0.5em;
29 }
30
31 div.tpR h3 {
32 font-family: sans-serif;
33 color: #000;
34 border-style: solid;
35 background-color: #fdd;
36 border-color: #f88;
37 border-width: 1px;
38 padding-left: 0.5em;
39 }
40 </style>
41 </head> 6 </head>
42 <body> 7 <body>
43 <div class="tpR"> 8 <div class="tpR">
44 <h1>Preprocessing</h1> 9 <h1>Preprocessing</h1>
45 <p> 10 <p>
46 Preprocessing of an `r datasetsource` DataSet, issued from 11 Preprocessing of an `r datasetsource` DataSet, issued from
47 `r technology` 12 `r technology`
48 technology. 13 technology.
49 </p> 14 </p>
50 <h2>Used methods for each step</h2> 15 <h2>Used methods for each step</h2>
51 16
52 <h3>Background correction methods</h3> 17 <h3>Background correction methods</h3>
53 <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre> 18 <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
54 <h3>Normalization methods</h3> 19 <h3>Normalization methods</h3>
55 <pre>method : `r listArguments[["normalization_method"]]`</pre> 20 <pre>method : `r listArguments[["normalization_method"]]`</pre>
56 <h3>Summarization methods</h3> 21 <h3>Summarization methods</h3>
57 <pre>method : `r listArguments[["summary_method"]]`</pre> 22 <pre>method : `r listArguments[["summary_method"]]`</pre>
58 <h2>Boxplots</h2> 23 <h2>Boxplots</h2>
59 <h3>Before NM</h3> 24 <h3>Before NM</h3>
60 <p> 25 <p>
61 <br> 26 <br>
62 <img src="boxplot_before_NM.png" width="100%" height="auto"> 27 <img src="boxplot_before_NM.png" width="100%" height="auto" alt="">
63 <br> 28 <br>
64 </p> 29 </p>
65 <h3>After NM</h3> 30 <h3>After NM</h3>
66 <p> 31 <p>
67 <br> 32 <br>
68 <img src="boxplot_after_NM.png" width="100%" height="auto"> 33 <img src="boxplot_after_NM.png" width="100%" height="auto" alt="">
69 <br> 34 <br>
70 </p> 35 </p>
71 <h2>MA plots</h2> 36 <h2>MA plots</h2>
72 <p> 37 <p>
73 <br> 38 <br>
74 <img src="MA_plot.png" width="100%" height="auto"> 39 <img src="MA_plot.png" width="100%" height="auto" alt="">
75 <br> 40 <br>
76 </p> 41 </p>
77 <h2>Densities plot</h2> 42 <h2>Densities plot</h2>
78 <h3>Before NM</h3> 43 <h3>Before NM</h3>
79 <p> 44 <p>
80 <br> 45 <br>
81 <img src="densities_plot_before_NM.png" width="100%" height="auto"> 46 <img src="densities_plot_before_NM.png" width="100%" height="auto" alt="">
82 <br> 47 <br>
83 </p> 48 </p>
84 <h3>After NM</h3> 49 <h3>After NM</h3>
85 <p> 50 <p>
86 <br> 51 <br>
87 <img src="densities_plot_after_NM.png" width="100%" height="auto"> 52 <img src="densities_plot_after_NM.png" width="100%" height="auto" alt="">
88 <br> 53 <br>
89 </p> 54 </p>
55 </div>
90 </body> 56 </body>
91 </html> 57 </html>