Mercurial > repos > ethevenot > batchcorrection
annotate determine_bc.xml @ 0:b74d1d533dea draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
author | ethevenot |
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date | Thu, 04 Aug 2016 11:40:35 -0400 |
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b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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1 <tool id="Determine_BC" name="Determine_batch_correction" version="2.0.0"> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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2 <description>to choose between linear, lowess and loess methods</description> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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3 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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4 <requirements> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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5 <requirement type="package" version="3.3.1">R</requirement> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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6 <requirement type="package">r-batch</requirement> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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7 <requirement type="package">r-ade4</requirement> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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8 <requirement type="package">r-pcaMethods</requirement> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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9 </requirements> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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10 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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11 <stdio> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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12 <exit_code range="1:" level="fatal" /> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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13 </stdio> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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14 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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15 <command><![CDATA[ |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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16 Rscript $__tool_directory__/batch_correction_wrapper.R |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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17 analyse "determine_bc" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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18 sampleMetadata "$sampleMetadata" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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19 dataMatrix "$dataMatrix" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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20 ref_factor "$ref_factor" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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21 #if str($advance.option ) == 'show': |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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22 span $advance.span |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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23 #else: |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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24 span "none" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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25 #end if |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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26 out_graph_pdf "$out_graph_pdf" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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27 out_preNormSummary "$out_preNormSummary" |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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28 ]]></command> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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29 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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30 <inputs> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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31 <param name="dataMatrix" type="data" label="Data Matrix file " help="" format="tabular" /> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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32 <param name="sampleMetadata" type="data" label="Sample metadata file " help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'" format="tabular" /> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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33 <param name="ref_factor" type="text" label="Factor of interest " help="column name of the factor of interest (often a biological factor); if none, leave 'batch'" value="batch" /> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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34 <conditional name="advance"> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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35 <param name="option" type="select" label="Advanced options" help="should only be put at 'show' if you have good understanding of the span parameter and are willing to adjust it"> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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36 <option value="show">show</option> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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37 <option value="hide" selected="true">hide</option> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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38 </param> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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39 <when value="hide"> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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40 <param name="span" type="hidden" value="none"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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41 </when> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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42 <when value="show"> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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43 <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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44 </when> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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45 </conditional> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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46 </inputs> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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47 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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48 <outputs> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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49 <data name="out_graph_pdf" label="Determine_BC_graph" format="pdf" ></data> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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50 <data name="out_preNormSummary" label="Determine_BC_preNormSummary" format="tabular" ></data> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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51 </outputs> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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52 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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53 <tests> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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54 <test> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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55 <param name="dataMatrix" value="input-determinebc-dataMatrix.tsv"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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56 <param name="sampleMetadata" value="input-determinebc-sampleMetadata.tsv"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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57 <param name="ref_factor" value="batch"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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58 <param name="option" value="hide"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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59 <param name="span" value="none"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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60 <output name="out_preNormSummary" file="output-determinebc-preNormSummary.txt"/> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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61 </test> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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62 </tests> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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63 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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64 <help> |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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65 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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66 .. class:: infomark |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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67 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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68 **Authors** Franck Giacomoni and Marion Landi (for interface and wrapper) and Jean-Francois Martin and Melanie Petera (for R) |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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69 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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70 --------------------------------------------------- |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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71 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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72 .. class:: infomark |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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73 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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74 **Please cite** If you use this tool, please cite `F.M. van der Kloet, I. Bobeldijk, E.R. Verheij, R.H. Jellema. (2009). "Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping." Journal of Proteome Research p5132-5141 <http://www.ncbi.nlm.nih.gov/pubmed/19754161>`_ |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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75 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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76 --------------------------------------------------- |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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77 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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78 ========================== |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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79 Determine_batch_correction |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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80 ========================== |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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81 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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82 ----------- |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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83 Description |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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84 ----------- |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
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85 |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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86 | Allows to choose between linear or non-linear (lowess or loess) functions for batch correction |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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87 | using quality control pooled samples (QC-pools) with correction algorithm as mentioned by Van Der Kloet (J Prot Res 2009). |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
parents:
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88 | |
b74d1d533dea
planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
ethevenot
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89 | Warning : this module does *not* deliver which choice should be made in model type; |
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90 | it only provides tools to help users to determine which choice may be appropriate, based on their own expertise. |
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91 | |
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92 | This tool is meant to be used prior to the Batch_correction tool to help make a choice in parameters, |
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93 | but it is not a requirement and thus can be avoided. |
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94 |
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95 |
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96 ----------------- |
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97 Workflow position |
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98 ----------------- |
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99 |
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100 .. image:: ./static/images/metabolomics/determine_batch_correction.png |
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101 :width: 800 |
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102 |
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103 |
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104 ----------- |
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105 Input files |
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106 ----------- |
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107 |
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108 +--------------------------+-----------+ |
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109 | Parameter : num + label | Format | |
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110 +==========================+===========+ |
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111 | 1 : Data Matrix file | tabular | |
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112 +--------------------------+-----------+ |
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113 | 2 : Sample metadata file | tabular | |
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114 +--------------------------+-----------+ |
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115 |
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116 |
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117 Data Matrix file must contain the intensity values of the variables. |
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118 | First line must contain all the samples' names |
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119 | First column must contain all the variables' ID |
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120 | |
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121 |
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122 Sample metadata file must contain at least the three following columns: |
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123 | "batch" to identify the batches of analyses |
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124 | "injectionOrder" (integers) defining the injection order of all samples (QC-pools as well as analysed samples) |
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125 | "sampleType" indicating if a sample ("sample") or a QC-pool ("pool"); each batch needs |
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126 | at least 3 QC-pools for intra-batch linear adjustment and 8 for lo(w)ess adjustment |
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127 |
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128 |
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129 .. class:: warningmark |
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130 |
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131 NO MISSING DATA are allowed |
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132 |
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133 |
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134 ---------- |
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135 Parameters |
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136 ---------- |
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137 |
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138 Factor of interest |
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139 | name of the factor (column header) that will be used as a categorical variable for plots. |
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140 | (often a biological factor ; if none, leave “batch”). |
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141 | This factor does not affect correction calculation. |
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142 | |
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143 |
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144 Advanced options |
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145 | should only be put at "show" if you have good understanding of the span parameter and are willing to adjust it. |
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146 | |
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147 |
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148 Span |
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149 | - when advanced option is at "hide" (default) |
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150 | default is 1 for loess regression and is two times the ratio between number of pools and number of samples for lowess regression. |
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151 | - when advanced option is at "show" : |
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152 | filled value is used for lowess and loess regression. |
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153 |
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154 |
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155 ------------ |
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156 Output files |
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157 ------------ |
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158 |
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159 Determine_BC_preNormSummary.tabular |
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160 | tabular output |
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161 | Meaning of results of diagnosis analysis |
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162 | 0 : no preliminary-condition problem |
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163 | 1 : standard deviation of QC-pools or samples = 0 |
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164 | 2 : insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess) |
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165 | 3 : significant difference between QC-pools and samples means |
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166 | 4 : denominator =0 when on 1 pool per batch non-0 |
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167 | 5 : (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2 |
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168 | |
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169 |
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170 Determine_BC_graph.pdf |
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171 | graphical output |
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172 | One page per ion. Plots regression curves for all methods allowed and plot.design results regarding the factor of interest. |
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173 |
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174 |
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175 --------------------------------------------------- |
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176 |
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177 --------------- |
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178 Working example |
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179 --------------- |
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180 |
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181 |
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182 .. class:: warningmark |
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183 |
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184 Soon see the corresponding "Page" |
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185 |
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186 |
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187 </help> |
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188 |
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189 <citations> |
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190 <citation type="bibtex">@Article{Kloet2009, |
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191 Title = {Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping}, |
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192 Author = {van der Kloet, Frans M. and Bobeldijk, Ivana and Verheij, Elwin R. and Jellema, Renger H.}, |
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193 Journal = {Journal of Proteome Research}, |
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194 Year = {2009}, |
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195 Note = {PMID: 19754161}, |
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196 Number = {11}, |
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197 Pages = {5132-5141}, |
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198 Volume = {8}, |
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199 |
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200 Doi = {10.1021/pr900499r}, |
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201 Url = {http://pubs.acs.org/doi/abs/10.1021/pr900499r} |
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202 }</citation> |
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203 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
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204 </citations> |
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205 |
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206 <!-- |
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207 Input files |
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208 =========== |
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209 |
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210 | **These two input files can be used in the purview "URL/Text:" of the tool "Get Data/Upload File",** |
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211 | **by checking the box "Convert spaces to tabs: YES"** |
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212 |
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213 Metadata_samples.txt |
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214 Model input Sample metadata file:: |
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215 |
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216 samples idLIMS serie factor01 factor02 batch injectionOrder sampleType |
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217 POOL1 POOL1 pool p pool 01_08_2011 1 p |
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218 X12588 12588 3 validation 2 01_08_2011 2 s |
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219 X17736 17736 3 Q1 1 01_08_2011 3 s |
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220 X15432 15432 3 validation 1 01_08_2011 4 s |
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221 X17159 17159 3 Q4 1 01_08_2011 5 s |
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222 X14325 14325 3 validation 2 01_08_2011 6 s |
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223 X17419 17419 3 Q4 1 01_08_2011 7 s |
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224 X16437 16437 3 Q4 1 01_08_2011 8 s |
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225 X16172 16172 3 Q4 2 01_08_2011 9 s |
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226 X16392 16392 3 Q4 2 01_08_2011 10 s |
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227 X13875 13875 3 validation 2 01_08_2011 11 s |
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228 POOL2 POOL2 pool p pool 01_08_2011 12 p |
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229 X13117 13117 3 Q4 2 01_08_2011 13 s |
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230 X13341 13341 3 Q1 2 01_08_2011 14 s |
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231 X16888 16888 3 Q4 1 01_08_2011 15 s |
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232 X17489 17489 3 Q4 2 01_08_2011 16 s |
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233 X12718 12718 3 Q1 2 01_08_2011 17 s |
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234 X16235 16235 3 Q4 2 01_08_2011 18 s |
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235 X16878 16878 3 Q1 1 01_08_2011 19 s |
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236 X12701 12701 3 validation 1 01_08_2011 20 s |
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237 X16220 16220 3 Q4 2 01_08_2011 21 s |
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238 X15635 15635 3 Q4 1 01_08_2011 22 s |
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239 |
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240 |
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241 Intensity_matrix.txt |
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242 Model input Matrix Ions file BEFORE IMPLEMENTATION:: |
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243 |
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244 samples POOL1 X12588 X17736 X15432 X17159 X14325 X17419 X16437 X16172 X16392 X13875 POOL2 X13117 X13341 X16888 X17489 X12718 X16235 X16878 X12701 X16220 X15635 |
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245 ion01 188.4140625 219.729126 122.5697632 123.5487671 805.8852539 183.4683838 37.33084106 151.8625488 97.12005615 91.24694824 69.87762451 195.4349365 112.4111938 136.7092285 159.9987793 172.1585693 0 117.5420532 133.6679688 80.05419922 160.0006104 760.0488281 |
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246 ion02 82.02575684 87.11358643 79.82391357 80.33862305 83.08575439 94.27703857 76.02288818 77.04394531 76.97564697 84.17669678 81.04943848 86.44024658 84.11865234 83.71282959 77.75219727 79.15936279 75.98492432 78.2835083 78.98760986 73.98388672 72.20550537 82.16448975 |
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247 ion03 25.31900024 24.2960968 23.29342651 31.54063416 30.3830719 22.42404175 35.44485474 26.38783264 17.1401825 21.27339172 20.25959778 26.33859253 18.17146301 26.32852173 24.30648804 28.34313965 29.37016296 18.23519897 24.48402405 25.38140869 24.35777283 21.31071472 |
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248 ion04 65.87536621 62.68716431 46.60232544 62.77856445 29.53218079 47.59136963 90.13983154 28.35336304 58.74325562 31.39331055 23.32928467 30.39666748 41.43960571 21.27049255 88.1161499 29.36820984 24.30200195 25.00007629 45.60662842 103.293457 37.46994019 87.09295654 |
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249 ion05 0 103.728544 279.5808214 884.2333448 824.5072072 434.6439081 764.82768 799.0972595 398.4002569 382.5370891 74.55342827 0 636.6596277 514.3863309 741.690017 412.3166491 660.8996555 57.36593795 102.2085264 455.6403091 548.6145486 515.8412195 |
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250 ion06 2711.785156 3465.292969 2469.75 3435.259766 2482.3125 2593.654297 1407.915039 1291.253906 2241.734375 1444.189453 3363.683594 2578.642578 2633.181641 3397.763672 3706.855469 3647.212891 3548.410156 3714.640625 1889.213867 2262.707031 2107.417969 2763.21875 |
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251 ion07 164.9023438 192.40625 140.7609863 192.4053955 139.7540283 140.748291 84.60144043 86.1819458 150.762207 89.90411377 207.5949707 164.0512695 149.8706055 186.336792 214.6140137 202.5360107 214.6877441 195.4482422 117.4679565 127.2941895 142.78479 163.0666504 |
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252 |
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253 |
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254 Parameters |
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255 ========== |
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256 |
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257 Factor analysis -> **batch** |
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258 |
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259 |
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260 Output files |
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261 ============ |
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262 |
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263 out_preNormSummary.tabular: |
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264 |
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265 ====== ============== ============== |
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266 labion batch.1.linear batch.1.lowess |
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267 ====== ============== ============== |
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268 ion01 2 2 |
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269 ion02 2 2 |
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270 ion03 2 2 |
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271 ion04 2 2 |
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272 ion05 1 1 |
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273 ... ... ... |
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274 ====== ============== ============== |
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275 |
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276 |
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277 out_graph_pdf.pdf |
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278 |
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279 .. image:: ./static/images/metabolomics/pdf_plotsituation.png |
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280 :width: 800 |
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281 --> |
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282 |
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283 </tool> |