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annotate test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 18:d9e7403f16f3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b3ba169290fd2e40dafe167f345106c1c3da3ebe
author lecorguille
date Wed, 08 Feb 2017 04:37:18 -0500
parents a2908411620e
children 3a53e63555c7
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a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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1 <!DOCTYPE html>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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2 <HTML lang='en'>
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3 <HEAD>
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4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
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5 <title>[W4M] XCMS analysis summary</title>
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6 <style>
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7 table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
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8 td,th { padding: 5px; padding-right: 12px; }
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9 th { background: #898989; text-align:left;color: white;}
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10 h2 { color: #FFA212; }
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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11 ul li { margin-bottom:10px; }
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12 </style>
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13 </HEAD>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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14 <BODY>
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15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
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16 </div>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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17 <h2>Samples used:</h2>
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18 <div><table>
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19 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
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20 <tr> <td> ko15 </td> <td> ./ko15.CDF </td> <td> 4698c36c0b3af007faf70975c04ccf2a </td> </tr><tr> <td> ko16 </td> <td> ./ko16.CDF </td> <td> afaeed94ced3140bc042d5ab6aeb16c1 </td> </tr><tr> <td> wt15 </td> <td> ./wt15.CDF </td> <td> d58a27fad7c04ddddb0359ddc2b7ba68 </td> </tr><tr> <td> wt16 </td> <td> ./wt16.CDF </td> <td> 29654e9f8ad48c1fbe2a41b9ba578f6e </td> </tr>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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21 </table>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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22 <br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were chancged during the process.
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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23 </div>
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24 <h2>Function launched:</h2>
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25 <div><table>
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26 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
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27 <tr><td rowspan='4'>170203-11:04:42</td><td rowspan='4'>xcmsSet</td>
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28 <td>nSlaves</td><td>1</td></tr>
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29 <tr><td>method</td><td>centWave</td></tr>
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30 <tr><td>ppm</td><td>25</td></tr>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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31 <tr><td>peakwidth</td><td>2050</td></tr>
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32 <tr><td rowspan='4'>170203-11:05:21</td><td rowspan='4'>xcmsSet</td>
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33 <td>nSlaves</td><td>1</td></tr>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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34 <tr><td>method</td><td>centWave</td></tr>
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35 <tr><td>ppm</td><td>25</td></tr>
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36 <tr><td>peakwidth</td><td>2050</td></tr>
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37 <tr><td rowspan='4'>170203-11:06:21</td><td rowspan='4'>xcmsSet</td>
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38 <td>nSlaves</td><td>1</td></tr>
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39 <tr><td>method</td><td>centWave</td></tr>
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40 <tr><td>ppm</td><td>25</td></tr>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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41 <tr><td>peakwidth</td><td>2050</td></tr>
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42 <tr><td rowspan='4'>170203-11:06:59</td><td rowspan='4'>xcmsSet</td>
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43 <td>nSlaves</td><td>1</td></tr>
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44 <tr><td>method</td><td>centWave</td></tr>
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45 <tr><td>ppm</td><td>25</td></tr>
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46 <tr><td>peakwidth</td><td>2050</td></tr>
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47 <tr><td rowspan='6'>170203-14:38:53</td><td rowspan='6'>group</td>
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48 <td>method</td><td>density</td></tr>
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49 <tr><td>sleep</td><td>0.001</td></tr>
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50 <tr><td>minfrac</td><td>0.3</td></tr>
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51 <tr><td>bw</td><td>5</td></tr>
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52 <tr><td>mzwid</td><td>0.01</td></tr>
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53 <tr><td>max</td><td>50</td></tr>
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54 <tr><td rowspan='7'>170203-14:51:16</td><td rowspan='7'>retcor</td>
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55 <td>method</td><td>peakgroups</td></tr>
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56 <tr><td>smooth</td><td>loess</td></tr>
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57 <tr><td>extra</td><td>1</td></tr>
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58 <tr><td>missing</td><td>1</td></tr>
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59 <tr><td>span</td><td>0.2</td></tr>
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60 <tr><td>family</td><td>gaussian</td></tr>
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61 <tr><td>plottype</td><td>deviation</td></tr>
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62 <tr><td rowspan='6'>170203-15:27:58</td><td rowspan='6'>group</td>
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63 <td>method</td><td>density</td></tr>
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64 <tr><td>sleep</td><td>0.001</td></tr>
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65 <tr><td>minfrac</td><td>0.3</td></tr>
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66 <tr><td>bw</td><td>5</td></tr>
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67 <tr><td>mzwid</td><td>0.01</td></tr>
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68 <tr><td>max</td><td>50</td></tr>
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69 <tr><td rowspan='5'>170203-15:44:50</td><td rowspan='5'>fillPeaks</td>
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70 <td>method</td><td>chrom</td></tr>
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71 <tr><td>convertRTMinute</td><td>FALSE</td></tr>
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72 <tr><td>numDigitsMZ</td><td>4</td></tr>
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73 <tr><td>numDigitsRT</td><td>1</td></tr>
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74 <tr><td>intval</td><td>into</td></tr>
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75 </table>
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76 <br/><sup>***</sup>timestamp format: yymmdd-hh:mm:ss
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77 </div>
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78 <h2>Informations about the xcmsSet object:</h2>
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79 <div><pre>
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80 An "xcmsSet" object with 4 samples
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81
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82 Time range: 2506-4484 seconds (41.8-74.7 minutes)
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83 Mass range: 200.1-600 m/z
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84 Peaks: 32720 (about 8180 per sample)
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85 Peak Groups: 8157
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86 Sample classes: KO, WT
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87
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88 Peak picking was performed on MS1.
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89 Profile settings: method = bin
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90 step = 0.1
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91
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92 Memory usage: 4.25 MB
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93 </pre></div>
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94 <h2>Citations:</h2>
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95 <div><ul>
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96 <li>To cite the <b>XCMS</b> package in publications use:
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97 <ul>
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98 <li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li>
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99 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
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100 <li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li>
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101 </ul>
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102 </li>
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103 <li>To cite the <b>CAMERA</b> package in publications use:
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104 <ul>
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105 <li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li>
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106 </ul>
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107 </li>
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108 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
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109 <ul>
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110 <li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813</li>
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111 </ul>
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112 </li>
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113 </ul></div>
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114 </BODY>
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115 </HTML>