Mercurial > repos > iuc > limma_voom

annotate limma_voom.xml @ 2:8a9806150b19 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
author iuc
date Thu, 07 Sep 2017 05:26:46 -0400
parents 3c8b816c26e7
children 895d310ddb21
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iuc
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1 <tool id="limma_voom" name="limma-voom" version="1.2.0">
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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2 <description>
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3 Differential expression with optional sample weights
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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4 </description>
1
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5
0
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6 <requirements>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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7 <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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8 <requirement type="package" version="3.30.13">bioconductor-limma</requirement>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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9 <requirement type="package" version="1.4.29">r-statmod</requirement>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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10 <requirement type="package" version="0.4.1">r-scales</requirement>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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11 </requirements>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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12
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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13 <version_command><![CDATA[
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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14 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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15 ]]></version_command>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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16
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17 <command detect_errors="exit_code"><![CDATA[
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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18 Rscript '$__tool_directory__/limma_voom.R'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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19 '$counts'
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20
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21 #if $anno.annoOpt=='yes':
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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22 '$geneanno'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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23 #else:
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24 None
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25 #end if
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26
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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27 '$outReport'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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28 '$outReport.files_path'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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29 $rdaOption
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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30 $normalisationOption
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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31 $weightOption
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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32 '$contrast'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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33
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34 #if $filterCPM.filterLowCPM=='yes':
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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35 '$filterCPM.cpmReq'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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36 '$filterCPM.sampleReq'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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37 #else:
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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38 0
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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39 0
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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40 #end if
0
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41
1
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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42 #if $testOpt.wantOpt=='yes':
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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43 '$testOpt.pAdjust'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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44 '$testOpt.pVal'
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45 '$testOpt.lfc'
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46 #else:
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47 "BH"
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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48 0.05
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49 0
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50 #end if
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51
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52 $normCounts
0
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53
1
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54 #if $fact.ffile=='yes':
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55 '$finfo'
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56 'None'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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57 #else:
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58 'None'
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59 '$fact.pfactName::$fact.pfactLevel'
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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60 #for $sfact in $fact.sfactors:
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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61 '$sfact.sfactName::$sfact.sfactLevel'
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62 #end for
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63 #end if
0
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64
1
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65 &&
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66 mkdir ./output_dir
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67
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68 &&
2
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69 cp '$outReport.files_path'/*.tsv output_dir/
1
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70 ]]></command>
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71
0
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72 <inputs>
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73 <param name="counts" type="data" format="tabular" label="Counts Data"/>
1
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74
0
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75 <conditional name="anno">
1
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76 <param name="annoOpt" type="select" label="Use Gene Annotations?"
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77 help="If an annotation file is provided, annotations will be added to the table of differential expression results to provide descriptions for each gene.">
0
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78 <option value="no">No</option>
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79 <option value="yes">Yes</option>
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80 </param>
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81 <when value="yes">
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82 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
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83 </when>
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84 <when value="no" />
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85 </conditional>
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86
1
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87 <conditional name="fact">
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88 <param name="ffile" type="select" label="Input Factor Information from file?"
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89 help="You can choose to input the factor information from a file or manually enter below.">
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90 <option value="no">No</option>
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91 <option value="yes">Yes</option>
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92 </param>
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93 <when value="yes">
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94 <param name="finfo" type="data" format="tabular" label="Factor Information"/>
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95 </when>
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96 <when value="no" >
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97 <param name="pfactName" type="text" label="Primary Factor Name"
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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98 help="Eg. Genotype NOTE: Please only use letters, numbers or underscores.">
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99 <validator type="empty_field" />
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100 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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101 </param>
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102 <param name="pfactLevel" type="text" label="Primary Factor Levels"
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103 help="Eg. WT,WT,WT,Mut,Mut,Mut NOTE: Please only use letters, numbers or underscores and ensure that the same levels are typed identically with cases matching.">
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104 <validator type="empty_field" />
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105 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
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106 </param>
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107 <repeat name="sfactors" title="Secondary Factor" >
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108 <param name="sfactName" type="text" label="Secondary Factor Name" help="Eg. Batch">
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109 <validator type="empty_field" />
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110 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
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111 </param>
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112 <param name="sfactLevel" type="text" label="Secondary Factor Levels"
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113 help="Eg. b1,b2,b3,b1,b2,b3 NOTE: Please only use letters, numbers or underscores and ensure that the same levels are typed identically with cases matching.">
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114 <validator type="empty_field" />
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115 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w,]+$</validator>
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116 </param>
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117 </repeat>
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118 </when>
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119 </conditional>
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120
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121 <param name="contrast" type="text" label="Contrasts of interest" help="Eg. Mut-WT,KD-Control">
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122 <validator type="empty_field" />
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123 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w,-]+$</validator>
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124 </param>
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125
0
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126 <conditional name="filterCPM">
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127 <param name="filterLowCPM" type="select" label="Filter Low CPM?"
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128 help="Treat genes with very low expression as unexpressed and filter out to speed up computation.">
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129 <option value="yes" selected="True">Yes</option>
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130 <option value="no">No</option>
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131 </param>
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132 <when value="yes">
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133 <param name="cpmReq" type="float" value="0.5" min="0" label="Minimum CPM"/>
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134 <param name="sampleReq" type="integer" value="1" min="0" label="Minimum Samples"
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135 help="Filter out all the genes that do not meet the minimum CPM in at least this many samples."/>
1
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136 </when>
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137 <when value="no"/>
0
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138 </conditional>
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139
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140 <param name="weightOption" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Apply sample weights?"
1
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141 help="Apply weights if outliers are present.">
0
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142 </param>
1
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143
0
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144 <param name="normalisationOption" type="select" label="Normalisation Method">
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145 <option value="TMM">TMM</option>
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146 <option value="RLE">RLE</option>
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147 <option value="upperquartile">Upperquartile</option>
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148 <option value="none">None (Don't normalise)</option>
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149 </param>
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150
1
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151 <param name="normCounts" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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152 label="Output normalised counts table?"
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153 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM).">
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154 </param>
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155
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156 <param name="rdaOption" type="boolean" truevalue="yes" falsevalue="no" checked="false"
0
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157 label="Output RData?"
1
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158 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report.">
0
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159 </param>
1
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160
0
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161 <conditional name="testOpt">
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162 <param name="wantOpt" type="select" label="Use Advanced Testing Options?"
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163 help="Enable choices for p-value adjustment method, p-value threshold and log2-fold-change threshold.">
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164 <option value="no" selected="True">No</option>
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165 <option value="yes">Yes</option>
1
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166 </param>
0
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167 <when value="yes">
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168 <param name="pAdjust" type="select" label="P-Value Adjustment Method.">
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169 <option value="BH">Benjamini and Hochberg (1995)</option>
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170 <option value="BY">Benjamini and Yekutieli (2001)</option>
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171 <option value="holm">Holm (1979)</option>
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172 <option value="none">None</option>
1
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173 </param>
0
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174 <param name="pVal" type="float" value="0.05" min="0" max="1"
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175 label="Adjusted Threshold"
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176 help="Genes below this threshold are considered significant and highlighted in the MA plot. If either BH(1995) or BY(2001) were selected then this value is a false-discovery-rate control. If Holm(1979) was selected then this is an adjusted p-value for family-wise error rate."/>
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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177 <param name="lfc" type="float" value="0" min="0"
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178 label="Minimum log2-fold-change Required"
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179 help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MA plot."/>
1
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180 </when>
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181 <when value="no"/>
0
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182 </conditional>
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183
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184 </inputs>
1
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185
0
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186 <outputs>
1
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187 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
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188 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
0
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189 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
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190 </collection>
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191 </outputs>
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192
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193 <tests>
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194 <test>
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195 <param name="counts" value="matrix.txt" />
1
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196 <param name="pfactName" value="Genotype" />
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197 <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
0
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198 <param name="contrast" value="Mut-WT,WT-Mut" />
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199 <param name="normalisationOption" value="TMM" />
1
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200 <output_collection name="outTables" count="2">
0
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201 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" />
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202 <element name="limma-voom_WT-Mut" ftype="tabular" file="limma-voom_WT-Mut.tsv" />
1
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203 </output_collection>
0
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204 <output name="outReport" >
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205 <assert_contents>
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206 <has_text text="Limma-voom Analysis Output" />
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207 <not_has_text text="RData" />
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208 </assert_contents>
1
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209 </output>
0
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210 </test>
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211 <test>
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212 <param name="annoOpt" value="yes" />
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213 <param name="geneanno" value="anno.txt" />
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214 <param name="counts" value="matrix.txt" />
1
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215 <param name="pfactName" value="Genotype" />
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216 <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
0
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217 <param name="contrast" value="Mut-WT" />
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218 <param name="normalisationOption" value="TMM" />
1
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219 <output_collection name="outTables" >
0
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220 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WTanno.tsv" />
1
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221 </output_collection>
0
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222 </test>
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223 <test>
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224 <param name="rdaOption" value="yes" />
1
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225 <param name="counts" value="matrix.txt" />
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226 <param name="pfactName" value="Genotype" />
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227 <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
0
bacbc977c562 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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228 <param name="contrast" value="Mut-WT" />
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229 <param name="normalisationOption" value="TMM" />
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230 <output name="outReport" >
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231 <assert_contents>
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232 <has_text text="RData" />
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233 </assert_contents>
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234 </output>
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235 </test>
1
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236 <test>
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237 <param name="counts" value="matrix.txt" />
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238 <param name="pfactName" value="Genotype"/>
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239 <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut"/>
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240 <repeat name="sfactors">
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241 <param name="sfactName" value="Batch"/>
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242 <param name="sfactLevel" value="b1,b2,b3,b1,b2,b3"/>
3c8b816c26e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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243 </repeat>
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diff changeset
244 <param name="contrast" value="Mut-WT" />
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diff changeset
245 <param name="normalisationOption" value="TMM" />
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246 <output_collection name="outTables" >
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diff changeset
247 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WTmultifact.tsv" />
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diff changeset
248 </output_collection>
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249 </test>
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250 <test>
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251 <param name="ffile" value="yes" />
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252 <param name="finfo" value="factorinfo.txt" />
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253 <param name="counts" value="matrix.txt" />
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254 <param name="contrast" value="Mut-WT" />
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255 <param name="normalisationOption" value="TMM" />
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256 <output_collection name="outTables" >
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257 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WTmultifact.tsv" />
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258 </output_collection>
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259 </test>
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260 <test>
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261 <param name="normCounts" value="yes" />
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262 <param name="counts" value="matrix.txt" />
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263 <param name="pfactName" value="Genotype" />
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264 <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
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265 <param name="contrast" value="Mut-WT" />
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266 <param name="normalisationOption" value="TMM" />
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267 <output_collection name="outTables" count="2">
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268 <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" />
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269 <element name="limma-voom_normcounts" ftype="tabular" file="limma-voom_normcounts.tsv" />
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270 </output_collection>
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271 </test>
0
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272 </tests>
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273
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274 <help><![CDATA[
0
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275 .. class:: infomark
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276
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277 **What it does**
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278
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279 Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool
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280 produces plots and tables useful in the analysis of differential gene
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281 expression.
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282
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283 -----
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284
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285 **Inputs**
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286
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287 **Counts Data:**
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288 A matrix of counts, with rows corresponding to genes
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289 and columns corresponding to counts for the samples.
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290 Values must be tab separated, with the first row containing the sample/column
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291 labels and the first column containing the row/gene labels.
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292
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293 Example:
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294
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295 ========== ======= ======= ======= ======== ======== ========
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296 **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
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297 ---------- ------- ------- ------- -------- -------- --------
1
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298 11287 1699 1528 1601 1463 1441 1495
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299 11298 1905 1744 1834 1345 1291 1346
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300 11302 6 8 7 5 6 5
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301 11303 2099 1974 2100 1574 1519 1654
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302 11304 356 312 337 361 397 346
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303 11305 2528 2438 2493 1762 1942 2027
0
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304 ========== ======= ======= ======= ======== ======== ========
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305
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306 **Gene Annotations:**
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307 Optional input for gene annotations, this can contain more
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308 information about the genes than just an ID number. The annotations will
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309 be available in the differential expression results table and the optional normalised counts table.
0
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310
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311 Example:
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312
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313 ========== ========== ===================================================
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314 **GeneID** **Symbol** **GeneName**
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315 ---------- ---------- ---------------------------------------------------
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316 1287 Pzp pregnancy zone protein
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317 1298 Aanat arylalkylamine N-acetyltransferase
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318 1302 Aatk apoptosis-associated tyrosine kinase
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319 1303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
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320 1304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
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321 1305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
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322 ========== ========== ===================================================
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323
1
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324 **Factor Information:**
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325 Enter Factor Names and Levels in the tool form or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the Primary Factor levels (e.g. Genotype) with optional additional columns for any Secondary Factors (e.g. Batch).
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326
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327 Example:
0
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328
1
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329 ========== ============ =========
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330 **Sample** **Genotype** **Batch**
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331 ---------- ------------ ---------
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332 WT1 WT b1
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333 WT2 WT b2
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334 WT3 WT b3
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335 Mut1 Mut b1
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336 Mut2 Mut b2
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337 Mut3 Mut b3
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338 ========== ============ =========
0
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339
1
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340 **Primary Factor Name:** The name of the primary factor being investigated e.g. Genotype. One primary factor must be entered and spaces must not be used.
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341
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342 **Primary Factor Levels:** The levels of the primary factor of interest, these must be entered in the same order as the samples to which the levels correspond, as listed in the columns of the counts matrix. Spaces must not be used and if entered in the tool form the values should be separated by commas.
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343
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344 **Secondary Factor Name:** Optionally, one or more secondary factors can be included. These are variables that might influence your experiment e.g. Batch, Gender. Spaces must not be used.
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345
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346 **Secondary Factor Levels:** The levels of the secondary factor of interest, these must be entered in the same order as the samples to which the levels correspond, as listed in the columns of the counts matrix. Spaces must not be used and if entered in the tool form the values should be separated by commas.
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347
0
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348
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349 **Contrasts of Interest:**
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350 The contrasts you wish to make between levels.
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351 A common contrast would be a simple difference between two levels: "Mut-WT"
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352 represents the difference between the mutant and wild type genotypes.
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353 Multiple contrasts should be separated by commas and spaces must not be used.
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354
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355 **Filter Low CPM:**
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356 Option to ignore the genes that do not show significant levels of
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357 expression, this filtering is dependent on two criteria:
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358
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359 * **Minimum CPM:** This is the counts per million that a gene must have in at
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360 least some specified number of samples.
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361
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362 * **Minumum Samples:** This is the number of samples in which the CPM
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363 requirement must be met in order for that gene to be acknowledged.
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364
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365 Only genes that exhibit a CPM greater than the required amount in at least the
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366 number of samples specified will be used for analysis. Care should be taken to
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367 ensure that the sample requirement is appropriate. In the case of an experiment
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368 with two experimental groups each with two members, if there is a change from
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369 insignificant cpm to significant cpm but the sample requirement is set to 3,
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370 then this will cause that gene to fail the criteria. When in doubt simply do not
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371 filter.
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372
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373 **Normalisation Method:**
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374 Option for using different methods to rescale the raw library
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375 size. For more information, see calcNormFactor section in the edgeR_ user's
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376 manual.
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377
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378 **Apply Sample Weights:**
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379 Option to downweight outlier samples such that their information is still
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380 used in the statistical analysis but their impact is reduced. Use this
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381 whenever significant outliers are present. The MDS plotting tool in this package
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382 is useful for identifying outliers. For more information on this option see Liu et al. (2015).
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383
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384 **Use Advanced Testing Options?:**
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385 By default error rate for multiple testing is controlled using Benjamini and
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386 Hochberg's false discovery rate control at a threshold value of 0.05. However
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387 there are options to change this to custom values.
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388
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389 * **P-Value Adjustment Method:**
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390 Change the multiple testing control method, the options are BH(1995) and
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391 BY(2001) which are both false discovery rate controls. There is also
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392 Holm(1979) which is a method for family-wise error rate control.
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393
0
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394 * **Adjusted Threshold:**
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395 Set the threshold for the resulting value of the multiple testing control
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396 method. Only observations whose statistic falls below this value is
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397 considered significant, thus highlighted in the MA plot.
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398
0
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399 * **Minimum log2-fold-change Required:**
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400 In addition to meeting the requirement for the adjusted statistic for
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401 multiple testing, the observation must have an absolute log2-fold-change
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402 greater than this threshold to be considered significant, thus highlighted
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403 in the MA plot.
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404
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405 **Outputs**
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406
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407 This tool outputs a table of differentially expressed genes for each contrast of interest and a HTML report with plots and additional information. Optionally you can choose to output the normalised counts table and the RData file.
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408
0
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409 -----
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410
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411 **Citations:**
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412
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413 .. class:: infomark
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414
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415 limma
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416
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417 Please cite the paper below for the limma software itself. Please also try
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418 to cite the appropriate methodology articles that describe the statistical
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419 methods implemented in limma, depending on which limma functions you are
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420 using. The methodology articles are listed in Section 2.1 of the limma
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421 User's Guide.
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422
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423 * Smyth GK (2005). Limma: linear models for microarray data. In:
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424 'Bioinformatics and Computational Biology Solutions using R and
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425 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
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426 W. Huber (eds), Springer, New York, pages 397-420.
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427
0
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428 * Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:
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429 precision weights unlock linear model analysis tools for
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430 RNA-seq read counts. Genome Biology 15, R29.
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431
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432 * Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.
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433
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434 * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
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435 A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
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436 for microarray data. BMC Bioinformatics 7, Article 261.
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437
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438 .. class:: infomark
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439
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440 edgeR
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441
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442 Please cite the first paper for the software itself and the other papers for
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443 the various original statistical methods implemented in edgeR. See
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444 Section 1.2 in the User's Guide for more detail.
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445
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446 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
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447 package for differential expression analysis of digital gene expression
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448 data. Bioinformatics 26, 139-140
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449
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450 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
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451 differences in tag abundance. Bioinformatics 23, 2881-2887
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452
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453 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
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454 binomial dispersion, with applications to SAGE data.
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455 Biostatistics, 9, 321-332
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456
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457 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
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458 of multifactor RNA-Seq experiments with respect to biological variation.
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459 Nucleic Acids Research 40, 4288-4297
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460
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461 Please report problems or suggestions to: su.s@wehi.edu.au
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462
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463 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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464 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
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465 ]]></help>
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466 <citations>
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467 <citation type="doi">10.1093/nar/gkv412</citation>
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468 </citations>
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469 </tool>