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comparison preprocess_datasets/Affymetrix.Rmd @ 36:0aa849aec11e draft

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author proteomisc
date Mon, 11 Dec 2023 19:37:42 +0000
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35:69a0a1cd02f5 36:0aa849aec11e
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6 </head> 323 </head>
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9 <h1>Preprocessing</h1> 326 <h1>Preprocessing</h1>
10 <p> 327 <p>
11 Preprocessing of an `r datasetsource` DataSet, issued from 328 Preprocessing of an `r datasetsource` DataSet, issued from
12 `r technology` 329 `r technology`
13 technology. 330 technology.
14 </p> 331 </p>
15 <h2>Used methods for each step</h2> 332 <h2>Used methods for each step</h2>
16 333
17 <h3>Background correction methods</h3> 334 <h3>Background correction methods</h3>
18 <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre> 335 <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
19 <h3>Normalization methods</h3> 336 <h3>Normalization methods</h3>
20 <pre>method : `r listArguments[["normalization_method"]]`</pre> 337 <pre>method : `r listArguments[["normalization_method"]]`</pre>
21 <h3>Summarization methods</h3> 338 <h3>Summarization methods</h3>
22 <pre>method : `r listArguments[["summary_method"]]`</pre> 339 <pre>method : `r listArguments[["summary_method"]]`</pre>
23 <h2>Boxplots</h2> 340 <h2>Boxplots</h2>
24 <h3>Before NM</h3> 341 <h3>Before NM</h3>
25 <p> 342 <p>
26 <br> 343 <br>
27 <img src="boxplot_before_NM.png" width="100%" height="auto" alt=""> 344 <img src="boxplot_before_NM.png" width="100%" height="auto">
28 <br> 345 <br>
29 </p> 346 </p>
30 <h3>After NM</h3> 347 <h3>After NM</h3>
31 <p> 348 <p>
32 <br> 349 <br>
33 <img src="boxplot_after_NM.png" width="100%" height="auto" alt=""> 350 <img src="boxplot_after_NM.png" width="100%" height="auto">
34 <br> 351 <br>
35 </p> 352 </p>
36 <h2>MA plots</h2> 353 <h2>MA plots</h2>
37 <p> 354 <p>
38 <br> 355 <br>
39 <img src="MA_plot.png" width="100%" height="auto" alt=""> 356 <img src="MA_plot.png" width="100%" height="auto">
40 <br> 357 <br>
41 </p> 358 </p>
42 <h2>Densities plot</h2> 359 <h2>Densities plot</h2>
43 <h3>Before NM</h3> 360 <h3>Before NM</h3>
44 <p> 361 <p>
45 <br> 362 <br>
46 <img src="densities_plot_before_NM.png" width="100%" height="auto" alt=""> 363 <img src="densities_plot_before_NM.png" width="100%" height="auto">
47 <br> 364 <br>
48 </p> 365 </p>
49 <h3>After NM</h3> 366 <h3>After NM</h3>
50 <p> 367 <p>
51 <br> 368 <br>
52 <img src="densities_plot_after_NM.png" width="100%" height="auto" alt=""> 369 <img src="densities_plot_after_NM.png" width="100%" height="auto">
53 <br> 370 <br>
54 </p> 371 </p>
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56 </body> 372 </body>
57 </html> 373 </html>