Mercurial > repos > lecorguille > xcms_summary

annotate test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 28:018a9771de28 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
author workflow4metabolomics
date Wed, 07 Apr 2021 16:46:50 +0000
parents db6549f27ad1
children 2a2850fdf29e
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27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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1 <!DOCTYPE html>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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2 <HTML lang='en'>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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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>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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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;}
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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10 h2 { color: #FFA212; }
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11 ul li { margin-bottom:10px; }
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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12 </style>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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13 </HEAD>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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14 <BODY>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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16 </div>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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17 <h2>Samples used:</h2>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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18 <div><table>
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19 <tr><th>sample</th><th>filename</th></tr>
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
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20 <tr><td>ko15</td><td>ko15.CDF</td></tr><tr><td>ko16</td><td>ko16.CDF</td></tr><tr><td>wt15</td><td>wt15.CDF</td></tr><tr><td>wt16</td><td>wt16.CDF</td></tr>
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27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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21 </table>
26
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
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22
12
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23 </div>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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24 <h2>Function launched:</h2>
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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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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db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
workflow4metabolomics
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27 <tr><td>Mon May 11 09:37:30 2020</td><td>Peak detection</td><td colspan='2'><pre>
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28 Object of class: CentWaveParam
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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29 Parameters:
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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30 ppm: 25
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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31 peakwidth: 20, 50
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32 snthresh: 10
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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33 prefilter: 3, 100
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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34 mzCenterFun: wMean
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35 integrate: 1
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 mzdiff: -0.001
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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37 fitgauss: FALSE
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38 noise: 0
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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39 verboseColumns: FALSE
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
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40 roiList length: 0
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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41 firstBaselineCheck TRUE
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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42 roiScales length: 0
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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43 </pre></td></tr>
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44 <tr><td>Mon May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre>
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45 Object of class: PeakDensityParam
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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46 Parameters:
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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47 sampleGroups: character of length 4
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48 bw: 5
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
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49 minFraction: 0.3
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97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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50 minSamples: 1
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51 binSize: 0.01
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52 maxFeatures: 50
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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53 </pre></td></tr>
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54 <tr><td>Mon May 11 09:38:08 2020</td><td>Retention time correction</td><td colspan='2'><pre>
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55 Object of class: PeakGroupsParam
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56 Parameters:
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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57 minFraction: 0.85
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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58 extraPeaks: 1
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59 smooth: loess
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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60 span: 0.2
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61 family: gaussian
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62 subset:
db6549f27ad1 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
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63 number of peak groups: 53
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64 </pre></td></tr>
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65 <tr><td>Mon May 11 09:38:09 2020</td><td>Peak grouping</td><td colspan='2'><pre>
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66 Object of class: PeakDensityParam
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67 Parameters:
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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68 sampleGroups: character of length 4
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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69 bw: 20
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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70 minFraction: 0.4
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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71 minSamples: 1
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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72 binSize: 0.25
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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73 maxFeatures: 50
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74 </pre></td></tr>
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75 <tr><td>Mon May 11 09:38:18 2020</td><td>Missing peak filling</td><td colspan='2'><pre>
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76 Object of class: FillChromPeaksParam
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77 Parameters:
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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78 expandMz: 0
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79 expandRt: 0
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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80 ppm: 0
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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81 </pre></td></tr>
12
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82 </table>
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83 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
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84 </div>
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85 <h2>Informations about the XCMSnExp object:</h2>
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86 <div><pre>
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87 MSn experiment data ("XCMSnExp")
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88 Object size in memory: 1.55 Mb
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89 - - - Spectra data - - -
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90 MS level(s): 1
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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91 Number of spectra: 5112
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92 MSn retention times: 41:38 - 75:7 minutes
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93 - - - Processing information - - -
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94 Data loaded [Mon May 11 09:37:30 2020]
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95 MSnbase version: 2.10.1
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96 - - - Meta data - - -
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97 phenoData
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98 rowNames: 1 2 3 4
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99 varLabels: sample_name sample_group
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100 varMetadata: labelDescription
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101 Loaded from:
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102 [1] ko15.CDF... [4] wt16.CDF
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103 Use 'fileNames(.)' to see all files.
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104 protocolData: none
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105 featureData
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106 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
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107 fvarLabels: fileIdx spIdx ... spectrum (31 total)
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108 fvarMetadata: labelDescription
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109 experimentData: use 'experimentData(object)'
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110 - - - xcms preprocessing - - -
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111 Chromatographic peak detection:
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112 method: centWave
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113 15405 peaks identified in 4 samples.
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114 On average 3851 chromatographic peaks per sample.
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115 Alignment/retention time adjustment:
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116 method: peak groups
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117 Correspondence:
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118 method: chromatographic peak density
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119 6349 features identified.
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120 Median mz range of features: 0
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121 Median rt range of features: 0
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122 6154 filled peaks (on average 1538.5 per sample).
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123 </pre></div>
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124 <h2>Informations about the xcmsSet object:</h2>
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125 <div><pre>
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126 An "xcmsSet" object with 4 samples
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127
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128 Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
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129 Mass range: 200.1-600 m/z
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130 Peaks: 15405 (about 3851 per sample)
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131 Peak Groups: 6349
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132 Sample classes: KO, WT
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133
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134 Feature detection:
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135 o Peak picking performed on MS1.
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136 o Scan range limited to 1 - 1278
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137 Profile settings: method = bin
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138 step = 0.1
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139
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140 Memory usage: 3.98 MB
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141 </pre></div>
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142 <h2>Citations:</h2>
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143 <div><ul>
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144 <li>To cite the <b>XCMS</b> package in publications use:
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145 <ul>
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146 <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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147 <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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148 <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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149 </ul>
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150 </li>
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151 <li>To cite the <b>CAMERA</b> package in publications use:
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152 <ul>
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153 <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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154 </ul>
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155 </li>
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156 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
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157 <ul>
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158 <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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159 </ul>
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160 </li>
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161 </ul></div>
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162 </BODY>
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163 </HTML>