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author lecorguille
date Fri, 19 Feb 2016 11:32:06 -0500
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1 <!DOCTYPE html>
2 <HTML lang='en'>
3 <HEAD>
4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
5 <title>[W4M] XCMS analysis summary</title>
6 <style>
7 table { min-width: 500px; border:1px solid #D6B161; border-collapse:collapse;}
8 th { background: #898989; text-align:left;}
9 tr { border: 1px solid #000000 }
10 h2 { color: #FFA212; }
11 ul li { margin-bottom:10px; }
12 </style>
13 </HEAD>
14 <BODY>
15 <h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
16 <h2>Samples used:</h2>
17 <table
18 <tr><th>sample</th><th>filename</th></tr>
19 <tr><td> HU_neg_051 </td><td> sacuri//bio2/HU_neg_051.mzXML </td></tr><tr><td> HU_neg_060 </td><td> sacuri//bio2/HU_neg_060.mzXML </td></tr><tr><td> HU_neg_017 </td><td> sacuri//bio/HU_neg_017.mzXML </td></tr><tr><td> HU_neg_028 </td><td> sacuri//bio/HU_neg_028.mzXML </td></tr><tr><td> Blanc04 </td><td> sacuri//blank/Blanc04.mzXML </td></tr><tr><td> Blanc06 </td><td> sacuri//blank/Blanc06.mzXML </td></tr>
20 </table>
21 <h2>Function launched:</h2>
22 <table>
23 <tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr>
24 <tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
25 <td>nSlaves</td><td>1</td></tr>
26 <tr><td>method</td><td>matchedFilter</td></tr>
27 <tr><td>step</td><td>0.01</td></tr>
28 <tr><td>fwhm</td><td>30</td></tr>
29 <tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td>
30 <td>method</td><td>density</td></tr>
31 <tr><td>sleep</td><td>0.001</td></tr>
32 <tr><td>minfrac</td><td>0.5</td></tr>
33 <tr><td>bw</td><td>30</td></tr>
34 <tr><td>mzwid</td><td>0.25</td></tr>
35 <tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
36 <td>method</td><td>chrom</td></tr>
37 </table>
38 <h2>Information about the xcmsSet object:</h2>
39 <pre>
40 An "xcmsSet" object with 6 samples
41
42 Time range: 16.3-1138.9 seconds (0.3-19 minutes)
43 Mass range: 61.9883-481.2446 m/z
44 Peaks: 1799 (about 300 per sample)
45 Peak Groups: 289
46 Sample classes: bio, bio2, blank
47
48 Profile settings: method = bin
49 step = 0.01
50
51 Memory usage: 0.421 MB
52 </pre>
53 <h2>Citations:</h2>
54 <ul>
55 <li>To cite the <b>XCMS</b> package in publications use:
56 <ul>
57 <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>
58 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
59 <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>
60 </ul>
61 </li>
62 <li>To cite the <b>CAMERA</b> package in publications use:
63 <ul>
64 <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>
65 </ul>
66 </li>
67 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
68 <ul>
69 <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>
70 </ul>
71 </li>
72 </ul>
73 </BODY>
74 </HTML>