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1 <tool id="Determine_BC" name="Determine_batch_correction" version="2.2.3">
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2 <description>to choose between linear, lowess and loess methods</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.1_4">r-batch</requirement>
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6 <requirement type="package" version="1.7_8">r-ade4</requirement>
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7 <requirement type="package" version="1.70.0">bioconductor-pcamethods</requirement>
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8 </requirements>
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9
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13
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14 <command><![CDATA[
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15 Rscript $__tool_directory__/batch_correction_wrapper.R
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16 analyse "determine_bc"
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17 sampleMetadata "$sampleMetadata"
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18 dataMatrix "$dataMatrix"
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19 ref_factor "$ref_factor"
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20 #if str($advance.option ) == 'show':
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21 span $advance.span
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22 #else:
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23 span "none"
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24 #end if
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25 out_graph_pdf "$out_graph_pdf"
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26 out_preNormSummary "$out_preNormSummary"
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27 ]]></command>
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28
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29 <inputs>
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30 <param name="dataMatrix" type="data" label="Data Matrix file " help="" format="tabular" />
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31 <param name="sampleMetadata" type="data" label="Sample metadata file " help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'" format="tabular" />
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32 <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" />
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33 <conditional name="advance">
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34 <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">
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35 <option value="show">show</option>
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36 <option value="hide" selected="true">hide</option>
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37 </param>
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38 <when value="show">
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39 <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/>
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40 </when>
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41 <when value="hide"/>
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42 </conditional>
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43 </inputs>
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44
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45 <outputs>
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46 <data name="out_graph_pdf" label="Determine_BC_graph" format="pdf" ></data>
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47 <data name="out_preNormSummary" label="Determine_BC_preNormSummary" format="tabular" ></data>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <param name="dataMatrix" value="input-determinebc-dataMatrix.tsv"/>
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53 <param name="sampleMetadata" value="input-determinebc-sampleMetadata.tsv"/>
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54 <param name="ref_factor" value="batch"/>
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55 <param name="option" value="hide"/>
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56 <param name="span" value="none"/>
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57 <output name="out_preNormSummary" file="output-determinebc-preNormSummary.txt"/>
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58 </test>
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59 </tests>
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60
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61 <help>
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62
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63 .. class:: infomark
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64
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65 **Authors**
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66 | Jean-Francois Martin - PF MetaToul-AXIOM ; INRA ; MetaboHUB (for original version of this tool and overall development of the R script)
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67
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68 .. class:: infomark
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69
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70 **Contributors**
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71 | Melanie Petera - PFEM ; INRA ; MetaboHUB (for R wrapper and R script improvement)
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72
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73 .. class:: infomark
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74
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75 **Wrapping**
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76 | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and R wrapper)
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77 | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface and R wrapper)
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78
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79 ---------------------------------------------------
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80
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81 .. class:: infomark
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82
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83 **Please cite** If you use this tool, please cite:
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84 | `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>`_
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85
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86 ---------------------------------------------------
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87
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88 ==========================
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89 Determine_batch_correction
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90 ==========================
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91
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92 -----------
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93 Description
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94 -----------
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95
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96 | Allows to choose between linear or non-linear (lowess or loess) functions for batch correction
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97 | using quality control pooled samples (QC-pools) with correction algorithm as mentioned by Van Der Kloet (J Prot Res 2009).
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98 |
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99 | Warning : this module does *not* deliver which choice should be made in model type;
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100 | it only provides tools to help users to determine which choice may be appropriate, based on their own expertise.
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101 |
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102 | This tool is meant to be used prior to the Batch_correction tool to help make a choice in parameters,
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103 | but it is not a requirement and thus can be avoided.
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104
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105
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106 -----------------
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107 Workflow position
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108 -----------------
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109
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110 .. image:: determine_batch_correction.png
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111 :width: 800
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112
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113
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114 -----------
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115 Input files
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116 -----------
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117
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118 +--------------------------+-----------+
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119 | Parameter : num + label | Format |
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120 +==========================+===========+
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121 | 1 : Data Matrix file | tabular |
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122 +--------------------------+-----------+
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123 | 2 : Sample metadata file | tabular |
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124 +--------------------------+-----------+
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125
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126
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127 Data Matrix file must contain the intensity values of the variables.
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128 | First line must contain all the samples' names
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129 | First column must contain all the variables' ID
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130 |
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131
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132 Sample metadata file must contain at least the three following columns:
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133 | "batch" to identify the batches of analyses
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134 | "injectionOrder" (integers) defining the injection order of all samples (QC-pools as well as analysed samples)
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135 | "sampleType" indicating if a sample ("sample") or a QC-pool ("pool"); each batch needs
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136 | at least 3 QC-pools for intra-batch linear adjustment and 8 for lo(w)ess adjustment
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137
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138
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139 .. class:: warningmark
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140
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141 NO MISSING DATA are allowed
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142
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143
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144 ----------
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145 Parameters
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146 ----------
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147
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148 Factor of interest
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149 | name of the factor (column header) that will be used as a categorical variable for plots.
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150 | (often a biological factor ; if none, leave “batch”).
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151 | This factor does not affect correction calculation.
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152 |
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153
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154 Advanced options
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155 | 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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156 |
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157
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158 Span
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159 | - when advanced option is at "hide" (default)
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160 | 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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161 | - when advanced option is at "show" :
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162 | filled value is used for lowess and loess regression.
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163
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164
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165 ------------
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166 Output files
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167 ------------
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168
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169 Determine_BC_preNormSummary.tabular
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170 | tabular output
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171 | Meaning of results of diagnosis analysis
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172 | 0 : no preliminary-condition problem
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173 | 1 : standard deviation of QC-pools or samples = 0
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174 | 2 : insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess)
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175 | 3 : significant difference between QC-pools and samples means
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176 | 4 : denominator =0 when on 1 pool per batch non-0
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177 | 5 : (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2
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178 |
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179
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180 Determine_BC_graph.pdf
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181 | graphical output
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182 | One page per ion. Plots regression curves for all methods allowed and plot.design results regarding the factor of interest.
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183
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184
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185 ---------------------------------------------------
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186
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187 ---------------
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188 Working example
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189 ---------------
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190
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191
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192 .. class:: warningmark
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193
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194 Refer to the corresponding "W4M HowTo" page:
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195 | `MS data processing - Filters and normalisation <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4e-2016-data_processing.pdf>`_
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196 |
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197 |
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198
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199
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200 </help>
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201
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202 <!-- [RECOMMANDED] All citations associated to this tool (main citation given above and other references). Can be extracted from the history panel -->
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203 <citations>
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204 <!-- [HELP] As DOI or BibTex entry -->
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205 <citation type="doi">10.1021/pr900499r</citation>
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206 </citations>
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207
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208 <!--
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209 Input files
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210 ===========
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211
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212 | **These two input files can be used in the purview "URL/Text:" of the tool "Get Data/Upload File",**
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213 | **by checking the box "Convert spaces to tabs: YES"**
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214
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215 Metadata_samples.txt
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216 Model input Sample metadata file::
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217
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218 samples idLIMS serie factor01 factor02 batch injectionOrder sampleType
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219 POOL1 POOL1 pool p pool 01_08_2011 1 p
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220 X12588 12588 3 validation 2 01_08_2011 2 s
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221 X17736 17736 3 Q1 1 01_08_2011 3 s
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222 X15432 15432 3 validation 1 01_08_2011 4 s
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223 X17159 17159 3 Q4 1 01_08_2011 5 s
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224 X14325 14325 3 validation 2 01_08_2011 6 s
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225 X17419 17419 3 Q4 1 01_08_2011 7 s
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226 X16437 16437 3 Q4 1 01_08_2011 8 s
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227 X16172 16172 3 Q4 2 01_08_2011 9 s
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228 X16392 16392 3 Q4 2 01_08_2011 10 s
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229 X13875 13875 3 validation 2 01_08_2011 11 s
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230 POOL2 POOL2 pool p pool 01_08_2011 12 p
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231 X13117 13117 3 Q4 2 01_08_2011 13 s
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232 X13341 13341 3 Q1 2 01_08_2011 14 s
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233 X16888 16888 3 Q4 1 01_08_2011 15 s
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234 X17489 17489 3 Q4 2 01_08_2011 16 s
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235 X12718 12718 3 Q1 2 01_08_2011 17 s
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236 X16235 16235 3 Q4 2 01_08_2011 18 s
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237 X16878 16878 3 Q1 1 01_08_2011 19 s
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238 X12701 12701 3 validation 1 01_08_2011 20 s
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239 X16220 16220 3 Q4 2 01_08_2011 21 s
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240 X15635 15635 3 Q4 1 01_08_2011 22 s
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241
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242
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243 Intensity_matrix.txt
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244 Model input Matrix Ions file BEFORE IMPLEMENTATION::
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245
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246 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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247 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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248 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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249 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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250 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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251 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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252 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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253 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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254
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255
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256 Parameters
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257 ==========
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258
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259 Factor analysis -> **batch**
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260
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261
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262 Output files
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263 ============
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264
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265 out_preNormSummary.tabular:
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266
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267 ====== ============== ==============
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268 labion batch.1.linear batch.1.lowess
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269 ====== ============== ==============
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270 ion01 2 2
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271 ion02 2 2
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272 ion03 2 2
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273 ion04 2 2
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274 ion05 1 1
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275 ... ... ...
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276 ====== ============== ==============
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277
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278
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279 out_graph_pdf.pdf
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280
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281 .. image:: ./static/images/metabolomics/pdf_plotsituation.png
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282 :width: 800
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283 -->
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284
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285 </tool>
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