Mercurial > repos > lecorguille > xcms_summary

annotate test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 40:00be6777edc5 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:15:21 -0400
parents 3d4339594010
children 5d59db39939a
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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; }
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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12 </style>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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18 <div><table>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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19 <tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
29
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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>
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a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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21 </table>
25
3a53e63555c7 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 392e432529877680e80a7b338e20d69a42e53767
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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 changed during the process.
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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23 </div>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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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>
29
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27 <tr><td>Wed Feb 7 11:15:25 2018</td><td>Peak detection</td><td colspan='2'><pre>
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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28 Object of class: CentWaveParam
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29 Parameters:
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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30 ppm: 25
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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31 peakwidth: 20, 50
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32 snthresh: 10
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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33 prefilter: 3, 100
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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34 mzCenterFun: wMean
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35 integrate: 1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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36 mzdiff: -0.001
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37 fitgauss: FALSE
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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38 noise: 0
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39 verboseColumns: FALSE
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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40 roiList length: 0
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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41 firstBaselineCheck TRUE
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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42 roiScales length: 0
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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43 </pre></td></tr>
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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44 <tr><td>Mon Feb 12 15:31:11 2018</td><td>Peak grouping</td><td colspan='2'><pre>
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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45 Object of class: PeakDensityParam
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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46 Parameters:
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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47 sampleGroups: character of length 4
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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48 bw: 30
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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49 minFraction: 0.8
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50 minSamples: 1
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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51 binSize: 0.25
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52 maxFeatures: 50
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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53 </pre></td></tr>
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54 <tr><td>Mon Feb 12 15:31:19 2018</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:
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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57 minFraction: 0.85
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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58 extraPeaks: 1
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59 smooth: loess
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60 span: 0.2
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61 family: gaussian
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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62 number of peak groups: 125
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63 </pre></td></tr>
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64 <tr><td>Mon Feb 12 15:31:27 2018</td><td>Peak grouping</td><td colspan='2'><pre>
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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65 Object of class: PeakDensityParam
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66 Parameters:
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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67 sampleGroups: character of length 4
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68 bw: 20
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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69 minFraction: 0.4
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70 minSamples: 1
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71 binSize: 0.25
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72 maxFeatures: 50
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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73 </pre></td></tr>
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74 <tr><td>Wed Feb 14 09:55:13 2018</td><td>Missing peak filling</td><td colspan='2'><pre>
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75 Object of class: FillChromPeaksParam
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76 Parameters:
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77 expandMz: 0
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78 expandRt: 0
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79 ppm: 0
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80 </pre></td></tr>
17
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81 </table>
29
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82 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
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83 </div>
29
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84 <h2>Informations about the XCMSnExp object:</h2>
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85 <div><pre>
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86 MSn experiment data ("XCMSnExp")
40
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87 Object size in memory: 1.41 Mb
29
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88 - - - Spectra data - - -
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89 MS level(s): 1
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90 Number of spectra: 5112
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91 MSn retention times: 41:33 - 75:0 minutes
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92 - - - Processing information - - -
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93 Concatenated [Thu Feb 8 15:36:09 2018]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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94 MSnbase version: 2.4.2
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95 - - - Meta data - - -
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96 phenoData
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97 rowNames: ./ko15.CDF ./ko16.CDF ./wt15.CDF ./wt16.CDF
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98 varLabels: sample_name sample_group
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99 varMetadata: labelDescription
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100 Loaded from:
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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101 [1] ko15.CDF... [4] wt16.CDF
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102 Use 'fileNames(.)' to see all files.
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103 protocolData: none
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104 featureData
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105 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
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106 fvarLabels: fileIdx spIdx ... spectrum (27 total)
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107 fvarMetadata: labelDescription
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108 experimentData: use 'experimentData(object)'
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109 - - - xcms preprocessing - - -
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110 Chromatographic peak detection:
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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111 method: centWave
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112 15230 peaks identified in 4 samples.
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113 On average 3808 chromatographic peaks per sample.
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114 Alignment/retention time adjustment:
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115 method: peak groups
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116 Correspondence:
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117 method: chromatographic peak density
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118 6332 features identified.
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119 Median mz range of features: 0
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120 Median rt range of features: 0
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121 5979 filled peaks (on average 1494.75 per sample).
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122 </pre></div>
17
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123 <h2>Informations about the xcmsSet object:</h2>
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124 <div><pre>
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125 An "xcmsSet" object with 4 samples
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126
29
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127 Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)
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128 Mass range: 200.1-600 m/z
29
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129 Peaks: 15230 (about 3808 per sample)
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130 Peak Groups: 6332
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131 Sample classes: KO, WT
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132
29
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133 Feature detection:
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134 o Peak picking performed on MS1.
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135 o Scan range limited to 1 - 1278
17
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136 Profile settings: method = bin
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137 step = 0.1
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138
40
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139 Memory usage: 3.11 MB
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140 </pre></div>
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141 <h2>Citations:</h2>
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142 <div><ul>
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143 <li>To cite the <b>XCMS</b> package in publications use:
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144 <ul>
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145 <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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146 <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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147 <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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148 </ul>
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149 </li>
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150 <li>To cite the <b>CAMERA</b> package in publications use:
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151 <ul>
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152 <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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153 </ul>
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154 </li>
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155 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
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156 <ul>
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157 <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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158 </ul>
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159 </li>
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160 </ul></div>
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161 </BODY>
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162 </HTML>