Mercurial > repos > workflow4metabolomics > xcms_refine

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<title>[W4M] XCMS analysis summary</title>
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<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
By: planemo@galaxyproject.org -
Date: 230525-08:53:25
</div>
<h2>Samples used:</h2>
<div><table>
<tr><th>sample</th><th>filename</th></tr>
<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>
</table>

</div>
<h2>Function launched:</h2>
<div><table>
<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
<tr><td>Mon May 11 09:37:30 2020</td><td>Peak detection</td><td colspan='2'><pre>
Object of class:  CentWaveParam
Parameters:
 ppm: 25
 peakwidth: 20, 50
 snthresh: 10
 prefilter: 3, 100
 mzCenterFun: wMean
 integrate: 1
 mzdiff: -0.001
 fitgauss: FALSE
 noise: 0
 verboseColumns: FALSE
 roiList length: 0
 firstBaselineCheck TRUE
 roiScales length: 0
</pre></td></tr>
<tr><td>Mon May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre>
Object of class:  PeakDensityParam
Parameters:
 sampleGroups: character of length 4
 bw: 5
 minFraction: 0.3
 minSamples: 1
 binSize: 0.01
 maxFeatures: 50
</pre></td></tr>
<tr><td>Mon May 11 09:38:08 2020</td><td>Retention time correction</td><td colspan='2'><pre>
Object of class:  PeakGroupsParam
Parameters:
 minFraction: 0.85
 extraPeaks: 1
 smooth: loess
 span: 0.2
 family: gaussian
 subset:
 number of peak groups: 53
</pre></td></tr>
<tr><td>Mon May 11 09:38:09 2020</td><td>Peak grouping</td><td colspan='2'><pre>
Object of class:  PeakDensityParam
Parameters:
 sampleGroups: character of length 4
 bw: 20
 minFraction: 0.4
 minSamples: 1
 binSize: 0.25
 maxFeatures: 50
</pre></td></tr>
<tr><td>Mon May 11 09:38:18 2020</td><td>Missing peak filling</td><td colspan='2'><pre>
Object of class:  FillChromPeaksParam
Parameters:
 expandMz: 0
 expandRt: 0
 ppm: 0
</pre></td></tr>
</table>
<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
</div>
<h2>Informations about the XCMSnExp object:</h2>
<div><pre>
MSn experiment data ("XCMSnExp")
Object size in memory: 1.55 Mb
- - - Spectra data - - -
 MS level(s): 1
 Number of spectra: 5112
 MSn retention times: 41:38 - 75:7 minutes
- - - Processing information - - -
Data loaded [Mon May 11 09:37:30 2020]
 MSnbase version: 2.10.1
- - - Meta data  - - -
phenoData
  rowNames: 1 2 3 4
  varLabels: sample_name sample_group
  varMetadata: labelDescription
Loaded from:
  [1] ko15.CDF...  [4] wt16.CDF
  Use 'fileNames(.)' to see all files.
protocolData: none
featureData
  featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
  fvarLabels: fileIdx spIdx ... spectrum (31 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
- - - xcms preprocessing - - -
Chromatographic peak detection:
 method: centWave
 15405 peaks identified in 4 samples.
 On average 3851 chromatographic peaks per sample.
Alignment/retention time adjustment:
 method: peak groups
Correspondence:
 method: chromatographic peak density
 6349 features identified.
 Median mz range of features: 0
 Median rt range of features: 0
 6154 filled peaks (on average 1538.5 per sample).
</pre></div>
<h2>Informations about the xcmsSet object:</h2>
<div><pre>
An "xcmsSet" object with 4 samples

Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
Mass range: 200.1-600 m/z
Peaks: 15405 (about 3851 per sample)
Peak Groups: 6349
Sample classes: KO, WT

Feature detection:
 o Peak picking performed on MS1.
 o Scan range limited to  1 - 1278
Profile settings: method = bin
                  step = 0.1

Memory usage: 3.98 MB
</pre></div>
<h2>Citations:</h2>
<div><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></div>
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author	workflow4metabolomics
date	Mon, 15 Jul 2024 16:00:52 +0000
parents	20f8ebc3a391
children