Mercurial > repos > lecorguille > anova
annotate galaxy/stat_anova/abims_anova.xml @ 8:c2be3b890724 draft
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date | Tue, 06 Jun 2017 09:43:23 -0400 |
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1 <tool id="abims_anova" name="Anova" version="1.1.4"> |
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2 |
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3 <description>N-way anova. With ou Without interactions</description> |
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5 <requirements> |
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6 <requirement type="package" version="1.1_4">r-batch</requirement> |
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7 </requirements> |
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8 |
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9 <stdio> |
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10 <exit_code range="1:" level="fatal" /> |
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11 </stdio> |
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12 |
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13 <command interpreter="Rscript"> |
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14 abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" |
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15 condition "c('$condition_1' |
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16 #for $i, $s in enumerate( $conditions ) |
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17 ,'${s.condition}' |
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18 #end for |
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19 )" |
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20 interaction $interaction method $method threshold $threshold selection_method $selection_method sep "$sep" dec "$dec" outputdatapvalue $dataMatrixPValue outputdatafiltered $dataMatrixFiltered |
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21 </command> |
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22 |
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23 <inputs> |
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24 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." /> |
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25 <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" /> |
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26 |
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27 <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true"> |
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28 <label>Mode</label> |
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29 <option value="row">row</option> |
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30 <option value="column">column</option> |
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31 </param> |
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32 |
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33 <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" /> |
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34 <repeat name="conditions" title="Conditions for N-ways anova"> |
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35 <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" /> |
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36 </repeat> |
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37 |
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38 <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" /> |
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39 |
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40 <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" format="text" optional="true"> |
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41 <label>PValue adjusted method</label> |
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42 <option value="BH">BH</option> |
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43 <option value="holm">holm</option> |
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44 <option value="bonferroni">bonferroni</option> |
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45 <option value="hochberg">hochberg</option> |
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46 <option value="hommel">hommel</option> |
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47 <option value="BY">BY</option> |
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48 <option value="fdr">fdr</option> |
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49 <option value="none">none</option> |
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50 </param> |
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51 |
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52 <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" /> |
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53 |
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54 <param name="selection_method" type="select" format="text" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. "> |
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55 <label>Selection method</label> |
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56 <option value="intersection" selected="true">intersection / strong</option> |
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57 <option value="union">union / weak</option> |
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58 </param> |
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59 |
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60 <param name="sep" type="select" format="text"> |
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61 <label>Separator of columns</label> |
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62 <option value="tabulation">tabulation</option> |
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63 <option value="semicolon">;</option> |
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64 <option value="comma">,</option> |
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65 </param> |
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66 |
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67 <param name="dec" type="text" label="Decimal separator" value="." help="" /> |
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68 |
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69 </inputs> |
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70 |
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71 <outputs> |
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72 <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/> |
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73 <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/> |
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74 </outputs> |
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75 |
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76 <tests> |
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77 <test> |
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78 <param name="input" value="dataMatrix.tsv"/> |
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79 <param name="sampleinfo" value="sampleMetadata.tsv"/> |
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80 <param name="mode" value="row"/> |
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81 <param name="condition_1" value="age"/> |
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82 <param name="conditions_0|condition" value="gender"/> |
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83 <param name="interaction" value="F"/> |
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84 <param name="method" value="BH"/> |
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85 <param name="threshold" value="0.05"/> |
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86 <param name="selection_method" value="union"/> |
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87 <param name="sep" value="tabulation"/> |
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88 <param name="dev" value="."/> |
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89 <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" /> |
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90 <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" /> |
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91 </test> |
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92 </tests> |
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93 |
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94 <help> |
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95 |
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96 .. class:: infomark |
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97 |
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98 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr |
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99 |
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100 --------------------------------------------------- |
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101 |
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102 ===== |
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103 Anova |
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104 ===== |
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105 |
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106 ----------- |
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107 Description |
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108 ----------- |
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109 |
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110 Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures, |
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111 in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation. |
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112 |
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113 |
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114 |
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115 ----------- |
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116 Input files |
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119 +---------------------------+------------+ |
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120 | Parameter : num + label | Format | |
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121 +===========================+============+ |
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122 | 1 : Data Matrix file | Tabular | |
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123 +---------------------------+------------+ |
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124 | 2 : Sample Metadata file | Tabular | |
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125 +---------------------------+------------+ |
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126 |
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127 |
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128 |
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129 ------------ |
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130 Output files |
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131 ------------ |
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132 |
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133 |
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134 |
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135 ***.anova_pvalue.tabular** |
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136 |
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137 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue). |
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138 |
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139 ***.anova_filtered.tabular** |
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140 |
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141 | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue. |
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142 |
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143 |
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144 ------ |
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145 |
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146 .. class:: infomark |
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147 |
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148 The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools: |
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149 | PCA |
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150 | Hierarchical Clustering |
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151 |
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152 |
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153 |
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154 --------------------------------------------------- |
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155 |
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156 --------------- |
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157 Working example |
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158 --------------- |
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159 |
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160 |
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161 Input files |
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162 ----------- |
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163 |
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164 **>A part of an example of Data Matrix file input** |
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165 |
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166 |
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167 +--------+------------------+----------------+ |
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168 | Name | Bur-eH_FSP_12 | Bur-eH_FSP_24 | |
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169 +========+==================+================+ |
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170 |M202T601| 91206595.7559783 |106808979.08546 | |
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171 +--------+------------------+----------------+ |
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172 |M234T851| 27249137.275504 |28824971.3177926| |
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173 +--------+------------------+----------------+ |
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174 |
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175 **>A part of an example of Sample Metadata file input** |
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176 |
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177 |
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178 +---------------------------+------------+------------+------------+ |
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179 | Sample name | class | time | batch | |
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180 +===========================+============+============+============+ |
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181 | Bur-eH_FSP_12 | Bur-eH | 12 | 1 | |
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182 +---------------------------+------------+------------+------------+ |
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183 | Bur-eH_FSP_24 | Bur-eH | 24 | 1 | |
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184 +---------------------------+------------+------------+------------+ |
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185 | Bur-NI_FSP_12 | Bur-NI | 12 | 2 | |
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186 +---------------------------+------------+------------+------------+ |
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187 | Bur-NI_FSP_24 | Bur-NI | 24 | 2 | |
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188 +---------------------------+------------+------------+------------+ |
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189 |
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190 Parameters |
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191 ---------- |
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192 |
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193 | Mode -> **row** |
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194 | column name of condition -> **class** |
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195 | Separator of columns: -> **tabulation** |
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196 | Decimal separator -> **.** |
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197 | PValue adjusted method -> **BH** |
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198 | Threshold -> **0.001** |
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199 |
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200 |
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201 |
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202 Output files |
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203 ------------ |
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204 |
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205 **Part of an example of xset.anova_filtered.tabular:** |
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206 |
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207 .. image:: anova_pvalue.png |
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208 |
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209 **Part of an example of xset.anova_pvalue.tabular:** |
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210 |
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211 .. image:: anova_filtered.png |
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212 |
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213 |
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214 --------------------------------------------------- |
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215 |
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216 |
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217 --------------------------- |
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218 Position in workflow4metabo |
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219 --------------------------- |
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220 |
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221 |
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222 **Upstream tools** |
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223 |
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224 +---------------------------+----------------------------------------+--------+------------------------+ |
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225 | Name | Output file | Format | parameter | |
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226 +===========================+========================================+========+========================+ |
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227 |xcms.diffreport |xset.diffreport.data_matrix.tsv | Tabular| Data table file | |
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228 +---------------------------+----------------------------------------+--------+------------------------+ |
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229 |CAMERA.annotateDiffreport |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file | |
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230 +---------------------------+----------------------------------------+--------+------------------------+ |
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231 |xcms.xcmsSet |sample_info.tab | Tabular| sample info table file | |
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232 +---------------------------+----------------------------------------+--------+------------------------+ |
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234 |
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235 **Downstream tools** |
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236 |
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237 +---------------------------+---------------------------------------------------------+--------+ |
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238 | Name | Output file | Format | |
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239 +===========================+=========================================================+========+ |
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240 |PCA |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular| |
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241 +---------------------------+---------------------------------------------------------+--------+ |
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242 |Hierarchical Clustering |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular| |
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243 +---------------------------+---------------------------------------------------------+--------+ |
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244 |
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245 |
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246 **General schema of the metabolomic workflow** |
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247 |
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248 .. image:: anova_workflow.png |
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250 </help> |
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252 <citations> |
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253 <citation>Ronald A. Fisher in the 1930s</citation> |
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254 </citations> |
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255 |
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256 </tool> |