Mercurial > repos > lecorguille > xcms_summary

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<title>[W4M] XCMS analysis summary</title>
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<h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
<h2>Samples used:</h2>
<table
<tr><th>sample</th><th>filename</th></tr>
<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>
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<h2>Function launched:</h2>
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<tr><th>timestamp<br />(ymd-h:m:s)</th><th>function</th><th>argument</th><th>value</th></tr>
<tr><td rowspan='4'>151221-16:20:54</td><td rowspan='4'>xcmsSet</td>
<td>nSlaves</td><td>1</td></tr>
<tr><td>method</td><td>matchedFilter</td></tr>
<tr><td>step</td><td>0.01</td></tr>
<tr><td>fwhm</td><td>30</td></tr>
<tr><td rowspan='5'>151221-16:37:00</td><td rowspan='5'>group</td>
<td>method</td><td>density</td></tr>
<tr><td>sleep</td><td>0.001</td></tr>
<tr><td>minfrac</td><td>0.5</td></tr>
<tr><td>bw</td><td>30</td></tr>
<tr><td>mzwid</td><td>0.25</td></tr>
<tr><td rowspan='1'>151221-16:37:20</td><td rowspan='1'>fillPeaks</td>
<td>method</td><td>chrom</td></tr>
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<h2>Information about the xcmsSet object:</h2>
<pre>
An "xcmsSet" object with 6 samples

Time range: 16.3-1138.9 seconds (0.3-19 minutes)
Mass range: 61.9883-481.2446 m/z
Peaks: 1799 (about 300 per sample)
Peak Groups: 289
Sample classes: bio, bio2, blank

Profile settings: method = bin
                  step = 0.01

Memory usage: 0.421 MB
</pre>
<h2>Citations:</h2>
<ul>
<li>To cite the <b>XCMS</b> package in publications use:
<ul>
<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>
<li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
<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>
</ul>
</li>
<li>To cite the <b>CAMERA</b> package in publications use:
<ul>
<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>
</ul>
</li>
<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
<ul>
<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>
</ul>
</li>
</ul>
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author	lecorguille
date	Mon, 22 Feb 2016 16:44:04 -0500
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