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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" />
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5 <title></title>
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6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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7 </head>
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8 <body>
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9 <div class="toolFormBody">
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10
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11 <div class="infomessage">Galaxy Tool "rglasso" run at 19/10/2014 13:11:14</div><br/>
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12 <div class="toolFormTitle">cox images and outputs</div>
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13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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14 <div><table class="simple" cellpadding="2" cellspacing="2">
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15 <tr>
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16 <td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf"><img src="cox_Coxglmnettest_glmnet_cvdeviance.png" title="Click to download a PDF of cox_Coxglmnettest_glmnet_cvdeviance.pdf" hspace="5" width="400"
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17 alt="Image called cox_Coxglmnettest_glmnet_cvdeviance.pdf"/></a></td>
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18
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19 <td><a href="cox_Coxglmnettest_glmnetdev.pdf"><img src="cox_Coxglmnettest_glmnetdev.png" title="Click to download a PDF of cox_Coxglmnettest_glmnetdev.pdf" hspace="5" width="400"
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20 alt="Image called cox_Coxglmnettest_glmnetdev.pdf"/></a></td>
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21 </tr>
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22
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23 </table></div>
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24
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25 <div class="toolFormTitle">cox log output</div>
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26
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27 <pre>
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28
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29 [1] "All partial likelihood coefficients from Cox model at minimum lambda of 0.00138091491730048:"
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30
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31 3 x 1 sparse Matrix of class "dgCMatrix"
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32
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33 1
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34
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35 rhubarb 1.124517e-03
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36
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37 vegemite 1.444990e-01
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38
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39 apple 3.344565e-06
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40
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41
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42 </pre>
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43
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44 <div class="toolFormTitle">rglasso log output</div>
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45
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46 <pre>
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47
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48 Loading required package: Matrix
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49
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50 Loading required package: methods
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51
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52 Loaded glmnet 1.9-8
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53
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54 Loaded lars 1.2
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55
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56 Warning messages:
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57
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58 1: In if (class(larsres) == "try-error") { :
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59
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60 the condition has length > 1 and only the first element will be used
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61
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62 2: In plot.window(...) : "label" is not a graphical parameter
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63
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64 3: In plot.xy(xy, type, ...) : "label" is not a graphical parameter
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65
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66 4: In axis(side = side, at = at, labels = labels, ...) :
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67
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68 "label" is not a graphical parameter
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69
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70 5: In axis(side = side, at = at, labels = labels, ...) :
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71
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72 "label" is not a graphical parameter
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73
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74 6: In box(...) : "label" is not a graphical parameter
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75
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76 7: In title(...) : "label" is not a graphical parameter
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77
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78
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79 </pre>
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80
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81 <div class="toolFormTitle">Other log output</div>
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82
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83 <pre>
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84
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85 ## Toolfactory generated command line = Rscript - None None
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86
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87 [1] Cox model: Got yvar= time,status cols 1 n preds= 3 forced in= 3
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88
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89 [2] Cox model: Got yvar= time,status cols 2 n preds= 3 forced in= 3
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90
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91 [1] Results preview:
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92
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93 regulator partial_likelihood forced_in glmnet_model best_lambda
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94
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95 rhubarb rhubarb 0.001180324 TRUE cox 0.01508333
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96
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97 vegemite vegemite 0.093827440 FALSE cox 0.01508333
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98
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99 [1] SessionInfo for this R session:
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100
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101 R version 3.1.0 (2014-04-10)
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102
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103 Platform: x86_64-unknown-linux-gnu (64-bit)
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104
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105 locale:
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106
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107 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
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108
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109 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
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110
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111 [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
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112
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113 attached base packages:
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114
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115 [1] methods stats graphics grDevices utils datasets base
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116
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117 other attached packages:
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118
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119 [1] lars_1.2 glmnet_1.9-8 Matrix_1.1-4
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120
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121 loaded via a namespace (and not attached):
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122
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123 [1] grid_3.1.0 lattice_0.20-29
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124
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125
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126 </pre>
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127
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128 <div class="toolFormTitle">All output files available for downloading</div>
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129
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130 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
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131
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132 <tr><td><a href="cox_Coxglmnettest_glmnet_cvdeviance.pdf">cox_Coxglmnettest_glmnet_cvdeviance.pdf</a></td><td>6.4 KB</td></tr>
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133 <tr class="odd_row"><td><a href="cox_Coxglmnettest_glmnetdev.pdf">cox_Coxglmnettest_glmnetdev.pdf</a></td><td>5.2 KB</td></tr>
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134 <tr><td><a href="cox_rglasso.log">cox_rglasso.log</a></td><td>228 B</td></tr>
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135 <tr class="odd_row"><td><a href="rglasso.Rscript">rglasso.Rscript</a></td><td>9.8 KB</td></tr>
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136 <tr><td><a href="rglasso_error.log">rglasso_error.log</a></td><td>671 B</td></tr>
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137 <tr class="odd_row"><td><a href="rglasso_runner.log">rglasso_runner.log</a></td><td>1.1 KB</td></tr>
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138 </table></div><br/>
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139 </div></body></html>
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140
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