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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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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://getgalaxy.org/" />
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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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11 <div class="infomessage">Galaxy Tool "DifferentialCounts" run at 06/10/2014 15:33:02</div><br/>
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12 <div class="toolFormTitle">DESeq2 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="DESeq2_DifferentialCounts_MA_plot.pdf"><img src="DESeq2_DifferentialCounts_MA_plot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_MA_plot.pdf" hspace="5" width="400"
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17 alt="Image called DESeq2_DifferentialCounts_MA_plot.pdf"/></a></td>
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18
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19 <td><a href="DESeq2_DifferentialCounts_PCA_plot.pdf"><img src="DESeq2_DifferentialCounts_PCA_plot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_PCA_plot.pdf" hspace="5" width="400"
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20 alt="Image called DESeq2_DifferentialCounts_PCA_plot.pdf"/></a></td>
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21
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22 <td><a href="DESeq2_DifferentialCounts_dispersion_estimates.pdf"><img src="DESeq2_DifferentialCounts_dispersion_estimates.png" title="Click to download a PDF of DESeq2_DifferentialCounts_dispersion_estimates.pdf" hspace="5" width="400"
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23 alt="Image called DESeq2_DifferentialCounts_dispersion_estimates.pdf"/></a></td>
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24 </tr>
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25 <tr>
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26 <td><a href="DESeq2_DifferentialCounts_qqplot.pdf"><img src="DESeq2_DifferentialCounts_qqplot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_qqplot.pdf" hspace="5" width="400"
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27 alt="Image called DESeq2_DifferentialCounts_qqplot.pdf"/></a></td>
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29 <td><a href="DESeq2_DifferentialCounts_sample_distance_plot.pdf"><img src="DESeq2_DifferentialCounts_sample_distance_plot.png" title="Click to download a PDF of DESeq2_DifferentialCounts_sample_distance_plot.pdf" hspace="5" width="400"
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30 alt="Image called DESeq2_DifferentialCounts_sample_distance_plot.pdf"/></a></td>
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31
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32 <td> </td>
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33 </tr></table></div>
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34
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35 <div class="toolFormTitle">DESeq2 log output</div>
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36
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37 <pre>
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38
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39 # DESeq top 50
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40
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41 Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL
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42
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43 Mir122a Mir122a 10112.31117 10.433687 0.3440661 30.324653 5.425198e-202 4.568017e-199 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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44
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45 Mir192 Mir192 271352.97636 6.994296 0.2346736 29.804353 3.430828e-195 1.444379e-192 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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46
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47 Mir149 Mir149 810.35429 -6.947219 0.2752144 -25.242938 1.353995e-140 3.800212e-138 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
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48
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49 Mir23a Mir23a 1289.18043 -3.104596 0.1650418 -18.810968 6.140634e-79 1.292603e-76 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
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50
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51 Mir204 Mir204 347.57397 -7.385478 0.4210055 -17.542475 6.790394e-69 1.143502e-66 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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52
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53 Mir10b Mir10b 27820.40551 -5.122625 0.3095281 -16.549791 1.606588e-61 2.254579e-59 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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54
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55 Mir194-2 Mir194-2 391.65678 5.272315 0.3261217 16.166709 8.660202e-59 1.041699e-56 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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56
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57 Mir181d Mir181d 275.22797 -3.578479 0.2232474 -16.029209 7.989327e-58 8.408767e-56 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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58
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59 Mir27a Mir27a 2788.72629 -3.022597 0.1992370 -15.170866 5.514410e-52 5.159037e-50 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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60
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61 Mir181c Mir181c 2765.96510 -3.678297 0.2459044 -14.958240 1.376168e-50 1.158734e-48 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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62
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63 Mir195 Mir195 519.86200 -3.158968 0.2124717 -14.867713 5.340712e-50 4.088073e-48 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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64
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65 Mir208b Mir208b 1649.77924 -12.247146 0.8586111 -14.263905 3.673137e-46 2.577318e-44 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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66
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67 Mir1948 Mir1948 263.89527 7.281854 0.5169425 14.086391 4.604994e-45 2.982619e-43 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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68
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69 Mir490 Mir490 220.99790 -8.314250 0.5954353 -13.963315 2.610066e-44 1.569768e-42 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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70
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71 Mir23b Mir23b 2028.55377 -2.066561 0.1531073 -13.497466 1.618477e-41 9.085049e-40 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
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72
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73 Mir21 Mir21 26121.31011 2.974199 0.2230949 13.331544 1.517256e-40 7.984558e-39 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
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74
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75 Mir101b Mir101b 6846.19683 3.823085 0.2899493 13.185354 1.065529e-39 5.277502e-38 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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76
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77 Mir208a Mir208a 616.76981 -11.025006 0.8475353 -13.008316 1.097341e-38 5.133115e-37 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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78
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79 Dnm3os Dnm3os 179.61643 -3.289322 0.2559302 -12.852417 8.336403e-38 3.694343e-36 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
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80
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81 Mir215 Mir215 152.78082 -3.012902 0.2351528 -12.812528 1.395132e-37 5.873506e-36 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
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82
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83 Mir214 Mir214 134.69038 -3.229468 0.2571076 -12.560766 3.469589e-36 1.391140e-34 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
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84
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85 Mir203 Mir203 772.92882 1.991755 0.1694325 11.755450 6.620692e-32 2.533919e-30 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
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86
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87 Mir499 Mir499 712.45950 -11.716229 1.0177724 -11.511639 1.152660e-30 4.219739e-29 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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88
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89 Mir27b Mir27b 76478.05753 -1.906131 0.1672784 -11.394959 4.430372e-30 1.554322e-28 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
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90
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91 Mir322 Mir322 899.53469 -3.147196 0.2773005 -11.349407 7.466726e-30 2.514793e-28 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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92
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93 Rabggtb Rabggtb 2257.19195 1.991117 0.1756753 11.334078 8.896442e-30 2.881079e-28 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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94
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95 Mir143hg Mir143hg 180217.77425 -2.173582 0.1966899 -11.050806 2.172555e-28 6.775153e-27 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
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96
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97 Mir143 Mir143 179219.35960 -2.174835 0.1975414 -11.009513 3.438555e-28 1.034023e-26 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
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98
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99 Mir378 Mir378 483.21548 -3.012592 0.2747646 -10.964266 5.675913e-28 1.647972e-26 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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100
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101 Mir132 Mir132 106.46062 -2.793901 0.2568175 -10.878935 1.452498e-27 4.076678e-26 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
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102
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103 Mir155 Mir155 57.66182 -3.815683 0.3605552 -10.582799 3.580985e-26 9.726416e-25 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
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104
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105 Mir24-2 Mir24-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
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106
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107 Mir3074-2 Mir3074-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
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108
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109 Mir125b-2 Mir125b-2 493.08516 -2.938770 0.2803125 -10.483910 1.024200e-25 2.536401e-24 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
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110
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111 Mir150 Mir150 553.20599 -2.856250 0.2760016 -10.348671 4.243363e-25 1.020832e-23 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
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112
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113 Mir182 Mir182 886.79583 5.089394 0.4937848 10.306907 6.557770e-25 1.533789e-23 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
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114
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115 Mir148a Mir148a 118994.46955 2.695116 0.2621094 10.282410 8.458605e-25 1.924904e-23 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
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116
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117 Mir199b Mir199b 47.84725 -5.417036 0.5304738 -10.211694 1.757697e-24 3.894687e-23 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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118
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119 Snord104 Snord104 3851.90119 2.396960 0.2371478 10.107451 5.119918e-24 1.105377e-22 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
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120
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121 Mir193 Mir193 45.70861 5.113887 0.5386870 9.493243 2.239557e-21 4.714267e-20 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
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122
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123 Mir200b Mir200b 87.13638 6.279428 0.6679043 9.401688 5.369454e-21 1.102703e-19 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
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124
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125 5430416N02Rik 5430416N02Rik 62.15966 3.116558 0.3399987 9.166382 4.891610e-20 9.806514e-19 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
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126
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127 Mir802 Mir802 166.83414 9.771028 1.0750153 9.089199 9.977106e-20 1.953657e-18 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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128
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129 Mir125b-1 Mir125b-1 79.01988 -3.046196 0.3356809 -9.074680 1.140124e-19 2.181783e-18 609 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
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130
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131 2610203C20Rik 2610203C20Rik 79.17666 -3.049266 0.3363186 -9.066600 1.227890e-19 2.297519e-18 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
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132
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133 Snord91a Snord91a 168.95251 2.722976 0.3035329 8.970941 2.939927e-19 5.381346e-18 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
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134
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135 Mir194-1 Mir194-1 71.10636 3.788463 0.4230333 8.955471 3.382877e-19 6.060389e-18 635 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'>Mir194-1</a>
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136
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137 Mir181a-1 Mir181a-1 59.53826 -3.173584 0.3580582 -8.863320 7.766622e-19 1.362395e-17 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
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138
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139 Mir181a-2 Mir181a-2 347.82506 -2.863247 0.3233431 -8.855136 8.358205e-19 1.436247e-17 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
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140
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141 Mir184 Mir184 32.23796 -4.996780 0.5668564 -8.814896 1.197967e-18 2.017377e-17 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
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142
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143
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144 </pre>
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145
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146 <div class="toolFormTitle">DifferentialCounts log output</div>
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147
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148 <pre>
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149
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150 KernSmooth 2.23 loaded
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151
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152 Copyright M. P. Wand 1997-2009
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153
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154 Attaching package: ‘gplots’
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155
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156 The following object is masked from ‘package:stats’:
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157
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158 lowess
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159
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160 Loading required package: limma
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161
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162 Loading required package: methods
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163
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164 Loading required package: splines
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165
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166 Loading required package: DESeq2
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167
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168 Loading required package: GenomicRanges
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169
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170 Loading required package: BiocGenerics
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171
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172 Loading required package: parallel
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173
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174 Attaching package: ‘BiocGenerics’
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175
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176 The following objects are masked from ‘package:parallel’:
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177
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178 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
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179
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180 The following object is masked from ‘package:limma’:
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181
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182 plotMA
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183
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184 The following object is masked from ‘package:stats’:
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185
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186 xtabs
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187
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188 The following objects are masked from ‘package:base’:
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189
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190 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
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191
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192 Loading required package: IRanges
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193
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194 Attaching package: ‘IRanges’
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195
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196 The following object is masked from ‘package:gplots’:
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197
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198 space
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199
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200 Loading required package: GenomeInfoDb
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201
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202 Loading required package: Rcpp
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203
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204 Loading required package: RcppArmadillo
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205
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206 gene-wise dispersion estimates
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207
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208 mean-dispersion relationship
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209
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210 final dispersion estimates
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211
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212 Warning messages:
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213
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214 1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == :
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215
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216 Outlier (-Inf) in boxplot 1 is not drawn
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217
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218 2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == :
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219
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220 Outlier (-Inf) in boxplot 3 is not drawn
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221
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222 3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067, :
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223
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224 some notches went outside hinges ('box'): maybe set notch=FALSE
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225
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226 4: In par(defpar) : calling par(new=TRUE) with no plot
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227
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228
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229 </pre>
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230
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231 <div class="toolFormTitle">VOOM images and outputs</div>
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232 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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233 <div><table class="simple" cellpadding="2" cellspacing="2">
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234 <tr>
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235 <td><a href="VOOM_DifferentialCounts_mean_variance_plot.pdf"><img src="VOOM_DifferentialCounts_mean_variance_plot.png" title="Click to download a PDF of VOOM_DifferentialCounts_mean_variance_plot.pdf" hspace="5" width="400"
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236 alt="Image called VOOM_DifferentialCounts_mean_variance_plot.pdf"/></a></td>
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237
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238 <td><a href="VOOM_DifferentialCounts_qqplot.pdf"><img src="VOOM_DifferentialCounts_qqplot.png" title="Click to download a PDF of VOOM_DifferentialCounts_qqplot.pdf" hspace="5" width="400"
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239 alt="Image called VOOM_DifferentialCounts_qqplot.pdf"/></a></td>
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240 </tr>
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241
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242 </table></div>
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243
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244 <div class="toolFormTitle">VOOM log output</div>
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245
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246 <pre>
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247
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248 # VOOM top 50
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249
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250 logFC AveExpr t P.Value adj.P.Val B NReads URL
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251
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252 Mir192 6.689950 14.4417888 50.335160 1.802287e-16 2.056409e-13 27.414844 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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253
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254 Mir208a -10.458438 3.8918506 -29.183545 2.249812e-13 1.283518e-10 19.141041 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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255
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256 Mir3073 8.318578 2.6485638 25.821264 1.102217e-12 4.192097e-10 18.063600 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
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257
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258 Mir802 8.992449 2.9857711 25.195575 1.514327e-12 4.319618e-10 17.906674 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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259
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260 Mir208b -12.256447 4.4678897 -22.360114 7.074494e-12 1.614400e-09 16.920424 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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261
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262 Mir499 -11.104485 3.8066799 -21.990054 8.769804e-12 1.667724e-09 16.728874 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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263
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264 Mir10b -4.775768 12.4173688 -21.487387 1.180685e-11 1.924516e-09 17.249348 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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265
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266 Mir148a 2.751538 15.4237642 20.289553 2.464883e-11 3.515539e-09 16.455471 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
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267
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268 Mir490 -8.497742 3.6613221 -18.336110 8.980482e-11 1.138526e-08 13.923237 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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269
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270 Mir122a 10.197963 8.1512374 17.467826 1.663427e-10 1.897970e-08 14.215445 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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271
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272 Mir133b -6.172367 1.3497975 -17.274094 1.916064e-10 1.987481e-08 13.840201 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
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273
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274 Mir149 -7.041176 6.0886889 -16.861286 2.602547e-10 2.474589e-08 13.714880 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
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275
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276 Mir101b 3.837883 10.6216725 15.443054 7.873164e-10 6.910215e-08 13.054350 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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277
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278 Mir143 -1.912927 16.0353646 -14.922755 1.209475e-09 9.857220e-08 12.374988 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
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279
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280 Mir194-2 5.534694 6.2627211 14.703097 1.455682e-09 1.107289e-07 12.316769 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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281
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282 Mir23a -2.905961 8.6431895 -14.558394 1.646894e-09 1.174441e-07 12.339306 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
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283
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284 Mir1983 -5.612359 1.1061384 -14.266537 2.119488e-09 1.422551e-07 11.743589 101 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
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285
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286 Mir27a -2.849084 10.0939084 -14.158498 2.329669e-09 1.476752e-07 11.960195 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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287
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288 Cyp3a25 6.312461 1.6425308 13.845627 3.074630e-09 1.846396e-07 11.502713 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
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289
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290 Mir200a 6.129125 1.8320913 13.226966 5.410979e-09 3.086963e-07 10.979834 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
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25
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291
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292 Mir181d -3.405544 6.3702152 -13.064584 6.300369e-09 3.423201e-07 11.006301 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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293
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294 Mir153 -5.698257 1.5328802 -12.832092 7.856705e-09 3.829623e-07 10.583835 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
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25
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295
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296 Mir204 -7.718081 4.5031856 -12.808496 8.036265e-09 3.829623e-07 10.353229 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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297
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298 Gm5441 -5.716851 1.5430406 -12.806028 8.055298e-09 3.829623e-07 10.562881 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
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299
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300 Rabggtb 2.327908 9.9369857 12.760291 8.416902e-09 3.841474e-07 10.654006 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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301
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302 Mir504 -5.122304 0.8161671 -12.391521 1.205304e-08 5.289430e-07 10.144865 69 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
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303
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304 Mir133a-1 -4.912497 0.7297882 -12.335045 1.274466e-08 5.385801e-07 10.076395 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
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305
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306 Mir195 -2.954216 7.3530970 -12.081859 1.641098e-08 6.603731e-07 10.055879 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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25
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307
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308 Mir27b -1.496991 14.9464877 -12.059553 1.678424e-08 6.603731e-07 9.674850 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
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309
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310 Snord52 2.631712 9.7652181 11.922618 1.928407e-08 7.334374e-07 9.811774 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
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311
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312 Mir322 -3.029558 8.1188344 -11.736839 2.333148e-08 8.587488e-07 9.679815 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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313
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314 Mir181c -3.676262 9.6244506 -11.575598 2.758358e-08 9.835271e-07 9.453057 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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315
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316 Mir1948 7.101780 4.7821564 11.471202 3.077353e-08 1.033009e-06 9.233632 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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317
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318 0610031O16Rik 4.519875 0.7388871 11.470939 3.078205e-08 1.033009e-06 9.284014 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
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319
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320 Mir201 -4.964105 0.7490919 -11.289794 3.729283e-08 1.210650e-06 9.114028 63 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir201'>Mir201</a>
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321
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322 Mir21 2.746616 13.2835800 11.267331 3.819755e-08 1.210650e-06 8.925217 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
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323
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324 Mir184 -5.569565 2.3521173 -11.190343 4.148052e-08 1.279170e-06 8.854599 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
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325
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326 1810019D21Rik 5.164581 1.0784751 11.082009 4.662057e-08 1.399844e-06 8.951908 117 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1810019D21Rik'>1810019D21Rik</a>
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327
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111
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328 Mir203 2.216791 8.5426169 10.866758 5.896538e-08 1.725115e-06 8.715639 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
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329
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330 1110038B12Rik 2.383720 10.6847245 10.832157 6.125623e-08 1.744094e-06 8.573067 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
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331
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111
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332 Snord104 2.571210 10.4798167 10.811468 6.267120e-08 1.744094e-06 8.561110 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
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333
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334 Mir182 5.196800 7.2088299 10.640454 7.579543e-08 2.021320e-06 8.545839 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
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335
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111
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336 Mir547 -4.542934 0.5799793 -10.635980 7.617593e-08 2.021320e-06 8.435473 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir547'>Mir547</a>
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337
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338 Mir143hg -2.291921 16.3789153 -10.597275 7.955395e-08 2.062978e-06 7.952584 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
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339
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340 Scnn1b -4.541403 0.5700621 -10.243065 1.190487e-07 3.018546e-06 8.023327 45 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scnn1b'>Scnn1b</a>
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341
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342 Mir125b-2 -2.896115 7.2737925 -10.091091 1.420082e-07 3.522420e-06 7.876068 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
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343
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344 Mir1a-1 -4.402568 0.4498447 -9.950346 1.675164e-07 4.066729e-06 7.692790 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-1'>Mir1a-1</a>
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345
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346 Mir378 -2.733247 7.2964165 -9.922980 1.730212e-07 4.112858e-06 7.672216 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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347
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348 Mir199b -5.651345 2.8029895 -9.883978 1.812024e-07 4.219426e-06 7.548022 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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349
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350 Mir155 -4.158272 3.8002361 -9.845490 1.896814e-07 4.328530e-06 7.604112 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
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351
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352
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353 </pre>
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354
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355 <div class="toolFormTitle">edgeR images and outputs</div>
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356 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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357 <div><table class="simple" cellpadding="2" cellspacing="2">
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358 <tr>
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359 <td><a href="edgeR_DifferentialCounts_BCV_vs_abundance.pdf"><img src="edgeR_DifferentialCounts_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_DifferentialCounts_BCV_vs_abundance.pdf" hspace="5" width="400"
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360 alt="Image called edgeR_DifferentialCounts_BCV_vs_abundance.pdf"/></a></td>
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361
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362 <td><a href="edgeR_DifferentialCounts_GoodnessofFit.pdf"><img src="edgeR_DifferentialCounts_GoodnessofFit.png" title="Click to download a PDF of edgeR_DifferentialCounts_GoodnessofFit.pdf" hspace="5" width="400"
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363 alt="Image called edgeR_DifferentialCounts_GoodnessofFit.pdf"/></a></td>
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364
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365 <td><a href="edgeR_DifferentialCounts_MDSplot.pdf"><img src="edgeR_DifferentialCounts_MDSplot.png" title="Click to download a PDF of edgeR_DifferentialCounts_MDSplot.pdf" hspace="5" width="400"
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366 alt="Image called edgeR_DifferentialCounts_MDSplot.pdf"/></a></td>
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367 </tr>
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368 <tr>
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369 <td><a href="edgeR_DifferentialCounts_qqplot.pdf"><img src="edgeR_DifferentialCounts_qqplot.png" title="Click to download a PDF of edgeR_DifferentialCounts_qqplot.pdf" hspace="5" width="400"
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370 alt="Image called edgeR_DifferentialCounts_qqplot.pdf"/></a></td>
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371
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372 <td><a href="edgeR_DifferentialCounts_raw_norm_counts_box.pdf"><img src="edgeR_DifferentialCounts_raw_norm_counts_box.png" title="Click to download a PDF of edgeR_DifferentialCounts_raw_norm_counts_box.pdf" hspace="5" width="400"
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373 alt="Image called edgeR_DifferentialCounts_raw_norm_counts_box.pdf"/></a></td>
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374
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375 <td><a href="edgeR_DifferentialCounts_smearplot.pdf"><img src="edgeR_DifferentialCounts_smearplot.png" title="Click to download a PDF of edgeR_DifferentialCounts_smearplot.pdf" hspace="5" width="400"
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376 alt="Image called edgeR_DifferentialCounts_smearplot.pdf"/></a></td>
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377 </tr>
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378 <tr>
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111
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379 <td><a href="edgeR_DifferentialCounts_top_100_heatmap.pdf"><img src="edgeR_DifferentialCounts_top_100_heatmap.png" title="Click to download a PDF of edgeR_DifferentialCounts_top_100_heatmap.pdf" hspace="5" width="400"
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380 alt="Image called edgeR_DifferentialCounts_top_100_heatmap.pdf"/></a></td>
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381
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382 <td> </td><td> </td>
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383 </tr></table></div>
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384
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385 <div class="toolFormTitle">edgeR log output</div>
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386
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387 <pre>
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388
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389 [1] Common Dispersion = 0.228651459675839 CV = 0.478175134940995 getPriorN = 3.33333333333333
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390
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391 [1] "No GLM fit outlier genes found\n"
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392
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111
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393 [1] Heart Liver
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394
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395 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
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396
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397 [1] raw contig counts by sample:
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398
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111
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399 Liver_X11706Liv_CAAA Liver_X11700Liv_ATTC Liver_X11698Liv_ACTG Liver_X11699Liv_ATGA Heart_X11706He_AGTTC Heart_X11699He_GGCTA Heart_X11698He_TAGCT Heart_X11700He_CTTGT
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25
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400
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401 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043
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402
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403 1st Qu.:0.3032 1st Qu.:0.0043 1st Qu.:0.3032 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043
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404
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405 Median :0.7789 Median :0.6031 Median :0.6998 Median :0.6031 Median :0.4786 Median :0.4786 Median :0.4786 Median :0.4786
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406
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407 Mean :1.0519 Mean :1.0343 Mean :0.9855 Mean :0.9966 Mean :0.9210 Mean :0.9428 Mean :1.0205 Mean :0.9753
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408
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409 3rd Qu.:1.5410 3rd Qu.:1.6335 3rd Qu.:1.4473 3rd Qu.:1.5534 3rd Qu.:1.5770 3rd Qu.:1.5855 3rd Qu.:1.7161 3rd Qu.:1.6022
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410
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411 Max. :5.8209 Max. :5.6905 Max. :5.7999 Max. :5.7215 Max. :5.3609 Max. :5.3589 Max. :5.6967 Max. :5.3702
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412
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413 NA's :650 NA's :969 NA's :664 NA's :886 NA's :902 NA's :957 NA's :821 NA's :950
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414
|
|
|
415 [1] normalised contig counts by sample:
|
|
|
416
|
|
111
|
417 Liver_X11706Liv_CAAA Liver_X11700Liv_ATTC Liver_X11698Liv_ACTG Liver_X11699Liv_ATGA Heart_X11706He_AGTTC Heart_X11699He_GGCTA Heart_X11698He_TAGCT Heart_X11700He_CTTGT
|
|
25
|
418
|
|
|
419 Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf
|
|
|
420
|
|
|
421 1st Qu.: 0 1st Qu.:-Inf 1st Qu.: 0 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf
|
|
|
422
|
|
|
423 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0
|
|
|
424
|
|
|
425 Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf
|
|
|
426
|
|
|
427 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1
|
|
|
428
|
|
|
429 Max. : 6 Max. : 6 Max. : 6 Max. : 5 Max. : 5 Max. : 5 Max. : 6 Max. : 5
|
|
|
430
|
|
|
431 [1] Using ncol rawrs= 8
|
|
|
432
|
|
|
433 [1] # edgeR Top tags\n
|
|
|
434
|
|
|
435 Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL
|
|
|
436
|
|
|
437 Mir208a Mir208a -11.840751 8.465017 594.16946 3.104543e-131 3.542284e-128 0.05171220 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
|
|
|
438
|
|
|
439 Mir149 Mir149 -7.008984 8.861767 484.30321 2.473909e-107 1.411365e-104 0.04959937 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
|
|
|
440
|
|
111
|
441 Mir208b Mir208b -13.291635 9.905945 417.69758 7.737466e-93 2.942816e-90 0.10508096 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
|
|
25
|
442
|
|
111
|
443 Mir122a Mir122a 10.514683 12.478088 415.17429 2.740528e-92 7.817355e-90 0.10803882 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
|
|
25
|
444
|
|
111
|
445 Mir204 Mir204 -7.498162 7.634507 341.30678 3.313429e-76 7.561245e-74 0.06907958 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
|
|
25
|
446
|
|
111
|
447 Mir499 Mir499 -13.577454 8.700078 325.79199 7.930762e-73 1.508166e-70 0.12042284 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
|
|
25
|
448
|
|
111
|
449 Mir490 Mir490 -8.534394 6.991023 303.17184 6.710365e-68 1.093790e-65 0.07949711 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
|
|
25
|
450
|
|
111
|
451 Mir192 Mir192 6.953853 17.169364 217.22866 3.638312e-49 5.189142e-47 0.12700995 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
|
|
25
|
452
|
|
111
|
453 Mir802 Mir802 11.440805 6.593380 212.88058 3.231647e-48 4.097010e-46 0.12273671 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
|
|
25
|
454
|
|
|
455 Mir1948 Mir1948 7.418142 7.252734 195.66958 1.840248e-44 2.099723e-42 0.12060221 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
|
|
|
456
|
|
|
457 Mir194-2 Mir194-2 5.298950 7.811522 191.85588 1.250960e-43 1.297587e-41 0.08670751 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
|
|
|
458
|
|
|
459 Mir23a Mir23a -3.153807 9.529402 177.53185 1.676248e-40 1.593833e-38 0.04442763 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
|
|
|
460
|
|
111
|
461 Mir181c Mir181c -3.767686 10.639598 169.87390 7.883296e-39 6.919108e-37 0.06368883 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
|
|
25
|
462
|
|
111
|
463 Mir3073 Mir3073 10.686337 5.859950 164.86740 9.778601e-38 7.969560e-36 0.14069249 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
|
|
25
|
464
|
|
|
465 Mir181d Mir181d -3.643963 7.300371 162.18591 3.767663e-37 2.865936e-35 0.05729574 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
|
|
|
466
|
|
|
467 Mir195 Mir195 -3.203683 8.215089 150.20548 1.563314e-34 1.114838e-32 0.05235020 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
|
|
|
468
|
|
111
|
469 Mir10b Mir10b -5.182616 13.946466 147.24792 6.926822e-34 4.649120e-32 0.12268790 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
|
|
25
|
470
|
|
111
|
471 Mir101b Mir101b 3.759962 11.863187 136.31359 1.703813e-31 1.080028e-29 0.07961343 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
|
|
25
|
472
|
|
|
473 Mir378 Mir378 -3.115599 8.119617 126.76408 2.092233e-29 1.256441e-27 0.05942391 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
|
|
|
474
|
|
111
|
475 Mir27a Mir27a -3.064687 10.642480 124.98911 5.117477e-29 2.919521e-27 0.06113852 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
|
|
25
|
476
|
|
|
477 Mir182 Mir182 5.057509 8.846381 123.17765 1.275060e-28 6.927826e-27 0.13653707 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
|
|
|
478
|
|
|
479 Mir322 Mir322 -3.194159 9.012888 107.34926 3.732413e-25 1.935765e-23 0.07536483 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
|
|
|
480
|
|
|
481 Mir199b Mir199b -5.520119 4.792610 102.10724 5.259607e-24 2.609223e-22 0.13417024 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
|
|
|
482
|
|
111
|
483 Mir181a-2 Mir181a-2 -3.000177 7.637692 101.38361 7.578821e-24 3.603098e-22 0.06896653 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
|
|
25
|
484
|
|
|
485 Mir125b-2 Mir125b-2 -2.987759 8.144514 91.72544 9.957640e-22 4.488356e-20 0.07737381 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
|
|
|
486
|
|
|
487 Dnm3os Dnm3os -3.331215 6.686950 91.67250 1.022763e-21 4.488356e-20 0.08810497 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
|
|
|
488
|
|
|
489 Mir184 Mir184 -5.111350 4.234160 84.35542 4.133639e-20 1.686711e-18 0.13502324 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
|
|
|
490
|
|
|
491 Mir215 Mir215 -3.058208 6.447966 84.35278 4.139167e-20 1.686711e-18 0.08138517 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
|
|
|
492
|
|
111
|
493 Mir133b Mir133b -8.383611 3.584760 83.96681 5.031521e-20 1.960318e-18 0.17482280 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
|
|
25
|
494
|
|
111
|
495 Mir150 Mir150 -2.883446 8.307765 83.91918 5.154209e-20 1.960318e-18 0.08008123 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
|
|
25
|
496
|
|
|
497 Mir3074-2 Mir3074-2 -2.778308 7.935651 83.74839 5.619282e-20 2.040616e-18 0.07424646 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
|
|
|
498
|
|
111
|
499 Mir24-2 Mir24-2 -2.778307 7.935651 83.71222 5.723023e-20 2.040616e-18 0.07427992 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
|
|
25
|
500
|
|
|
501 Mir193 Mir193 5.176579 4.801090 83.19222 7.445011e-20 2.574169e-18 0.14794861 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
|
|
|
502
|
|
|
503 Scarna17 Scarna17 2.182159 9.244479 81.91330 1.421894e-19 4.771710e-18 0.04982909 9224 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a>
|
|
|
504
|
|
111
|
505 Mir214 Mir214 -3.271172 6.271755 80.43948 2.997457e-19 9.771711e-18 0.09566584 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
|
|
25
|
506
|
|
111
|
507 Snord104 Snord104 2.330488 11.053611 79.50529 4.809370e-19 1.524303e-17 0.05915990 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
|
|
25
|
508
|
|
|
509 Mir200a Mir200a 7.201555 4.139422 77.35503 1.428304e-18 4.365755e-17 0.19287764 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
|
|
|
510
|
|
|
511 Mir200b Mir200b 6.525423 5.752604 77.31985 1.453976e-18 4.365755e-17 0.26237966 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
|
|
|
512
|
|
111
|
513 Mir21 Mir21 2.923147 13.825255 75.51798 3.620939e-18 1.059357e-16 0.09395834 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
|
|
25
|
514
|
|
|
515 Mir203 Mir203 1.956427 8.767610 75.17870 4.299815e-18 1.226522e-16 0.04381710 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
|
|
|
516
|
|
|
517 Mir155 Mir155 -3.886731 5.068563 73.81316 8.587210e-18 2.389758e-16 0.12522673 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
|
|
|
518
|
|
111
|
519 Cyp3a25 Cyp3a25 8.681501 3.972085 72.29680 1.851472e-17 5.029834e-16 0.23125383 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
|
|
25
|
520
|
|
111
|
521 Rabggtb Rabggtb 1.934093 10.298211 72.02043 2.129809e-17 5.651423e-16 0.04596646 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
|
|
25
|
522
|
|
111
|
523 Mir23b Mir23b -2.100584 10.184110 71.44225 2.854936e-17 7.403367e-16 0.05416378 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
|
|
25
|
524
|
|
111
|
525 Snord52 Snord52 2.207491 10.217554 71.27974 3.100028e-17 7.860292e-16 0.05941483 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
|
|
25
|
526
|
|
111
|
527 Gm5441 Gm5441 -6.881248 3.538457 70.05615 5.764005e-17 1.429724e-15 0.20097284 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
|
|
25
|
528
|
|
111
|
529 Mir153 Mir153 -6.857671 3.517446 69.37600 8.137283e-17 1.975455e-15 0.20158808 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
|
|
25
|
530
|
|
|
531 Mir132 Mir132 -2.858294 5.938312 64.52507 9.531204e-16 2.265647e-14 0.09274248 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
|
|
|
532
|
|
|
533 1110038B12Rik 1110038B12Rik 2.195962 11.253090 62.92015 2.152583e-15 5.012443e-14 0.06712174 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
|
|
|
534
|
|
|
535 Snord91a Snord91a 2.654072 6.557504 62.40549 2.795431e-15 6.379174e-14 0.08637410 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
|
|
|
536
|
|
|
537 [1] # 416 tags significant at adj p= 0.05
|
|
|
538
|
|
|
539
|
|
|
540 </pre>
|
|
|
541
|
|
|
542 <div class="toolFormTitle">Other images and outputs</div>
|
|
|
543 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
|
|
|
544 <div><table class="simple" cellpadding="2" cellspacing="2">
|
|
|
545 <tr>
|
|
|
546 <td><a href="Filtering_rowsum_bar_charts.pdf"><img src="Filtering_rowsum_bar_charts.png" title="Click to download a PDF of Filtering_rowsum_bar_charts.pdf" hspace="5" width="400"
|
|
|
547 alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td>
|
|
|
548
|
|
111
|
549 <td><a href="Venn_DifferentialCounts_significant_genes_overlap.pdf"><img src="Venn_DifferentialCounts_significant_genes_overlap.png" title="Click to download a PDF of Venn_DifferentialCounts_significant_genes_overlap.pdf" hspace="5" width="400"
|
|
|
550 alt="Image called Venn_DifferentialCounts_significant_genes_overlap.pdf"/></a></td>
|
|
25
|
551 </tr>
|
|
|
552 <tr>
|
|
|
553 <td><a href="sample_counts_histogram.pdf"><img src="sample_counts_histogram.png" title="Click to download a PDF of sample_counts_histogram.pdf" hspace="5" width="400"
|
|
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554 alt="Image called sample_counts_histogram.pdf"/></a></td>
|
|
|
555
|
|
|
556 <td> </td>
|
|
|
557 </tr></table></div>
|
|
|
558
|
|
|
559 <div class="toolFormTitle">Other log output</div>
|
|
|
560
|
|
|
561 <pre>
|
|
|
562
|
|
|
563 ## Toolfactory generated command line = Rscript - None None
|
|
|
564
|
|
|
565 Got TCols=1 5 6 7; CCols=2 3 4 8
|
|
|
566
|
|
|
567 [1] # Quantiles for non-zero row counts:
|
|
|
568
|
|
|
569 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|
|
|
570
|
|
|
571 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0
|
|
|
572
|
|
|
573 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
|
|
|
574
|
|
|
575 [1] "@@ using genecards substitution for urls"
|
|
|
576
|
|
111
|
577 [1] # urls sample
|
|
25
|
578
|
|
|
579 [1] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'>0610005C13Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'>0610007N19Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'>0610008F07Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'>0610009L18Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'>0610012G03Rik</a>
|
|
|
580
|
|
|
581 [6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
|
|
|
582
|
|
111
|
583 [1] # Total low count contigs per sample = 1 # Total low count contigs per sample = 1 # Total low count contigs per sample = 1 # Total low count contigs per sample = 1 # Total low count contigs per sample = 1 # Total low count contigs per sample = 1 # Total low count contigs per sample = 1 # Total low count contigs per sample = 1
|
|
25
|
584
|
|
111
|
585 [1] Using samples: Liver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,Liver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,Liver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,Liver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam,Heart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,Heart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,Heart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,Heart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam
|
|
25
|
586
|
|
|
587 [1] Using design matrix:
|
|
|
588
|
|
111
|
589 (Intercept) groupLiver
|
|
25
|
590
|
|
|
591 1 1 1
|
|
|
592
|
|
|
593 2 1 1
|
|
|
594
|
|
|
595 3 1 1
|
|
|
596
|
|
|
597 4 1 1
|
|
|
598
|
|
|
599 5 1 0
|
|
|
600
|
|
|
601 6 1 0
|
|
|
602
|
|
|
603 7 1 0
|
|
|
604
|
|
|
605 8 1 0
|
|
|
606
|
|
|
607 attr(,"assign")
|
|
|
608
|
|
|
609 [1] 0 1
|
|
|
610
|
|
|
611 attr(,"contrasts")
|
|
|
612
|
|
|
613 attr(,"contrasts")$group
|
|
|
614
|
|
|
615 [1] contr.treatment
|
|
|
616
|
|
111
|
617 R version 3.1.0 (2014-04-10)
|
|
25
|
618
|
|
|
619 Platform: x86_64-unknown-linux-gnu (64-bit)
|
|
|
620
|
|
|
621 locale:
|
|
|
622
|
|
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623 [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
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624
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625 attached base packages:
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626
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627 [1] parallel splines methods stats graphics grDevices utils datasets base
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628
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629 other attached packages:
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630
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631 [1] RColorBrewer_1.0-5 DESeq2_1.4.5 RcppArmadillo_0.4.400.0 Rcpp_0.11.2 GenomicRanges_1.16.4 GenomeInfoDb_1.0.2 IRanges_1.22.10 BiocGenerics_0.10.0 edgeR_3.6.8 limma_3.20.9 gplots_2.14.1 stringr_0.6.2
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632
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633 loaded via a namespace (and not attached):
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634
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635 [1] annotate_1.42.1 AnnotationDbi_1.26.0 Biobase_2.24.0 bitops_1.0-6 caTools_1.17 DBI_0.2-7 gdata_2.13.3 genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.0 gtools_3.4.1 KernSmooth_2.23-12 lattice_0.20-29 locfit_1.5-9.1 RSQLite_0.11.4 stats4_3.1.0 survival_2.37-7 XML_3.98-1.1 xtable_1.7-3 XVector_0.4.0
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636
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637
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638 </pre>
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639
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640 <div class="toolFormTitle">All output files available for downloading</div>
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641
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642 <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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643
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644 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr>
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645 <tr class="odd_row"><td><a href="DESeq2_DifferentialCounts_MA_plot.pdf">DESeq2_DifferentialCounts_MA_plot.pdf</a></td><td>14.9 KB</td></tr>
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646 <tr><td><a href="DESeq2_DifferentialCounts_PCA_plot.pdf">DESeq2_DifferentialCounts_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
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647 <tr class="odd_row"><td><a href="DESeq2_DifferentialCounts_dispersion_estimates.pdf">DESeq2_DifferentialCounts_dispersion_estimates.pdf</a></td><td>188.4 KB</td></tr>
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648 <tr><td><a href="DESeq2_DifferentialCounts_qqplot.pdf">DESeq2_DifferentialCounts_qqplot.pdf</a></td><td>12.8 KB</td></tr>
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649 <tr class="odd_row"><td><a href="DESeq2_DifferentialCounts_sample_distance_plot.pdf">DESeq2_DifferentialCounts_sample_distance_plot.pdf</a></td><td>9.4 KB</td></tr>
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650 <tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>28.4 KB</td></tr>
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651 <tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>2.0 KB</td></tr>
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652 <tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.5 KB</td></tr>
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653 <tr class="odd_row"><td><a href="Filtering_rowsum_bar_charts.pdf">Filtering_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>
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654 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>9.4 KB</td></tr>
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655 <tr class="odd_row"><td><a href="VOOM_DifferentialCounts_mean_variance_plot.pdf">VOOM_DifferentialCounts_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>
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656 <tr><td><a href="VOOM_DifferentialCounts_qqplot.pdf">VOOM_DifferentialCounts_qqplot.pdf</a></td><td>17.5 KB</td></tr>
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657 <tr class="odd_row"><td><a href="Venn_DifferentialCounts_significant_genes_overlap.pdf">Venn_DifferentialCounts_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>
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658 <tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr>
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659 <tr class="odd_row"><td><a href="edgeR_DifferentialCounts_BCV_vs_abundance.pdf">edgeR_DifferentialCounts_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
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660 <tr><td><a href="edgeR_DifferentialCounts_GoodnessofFit.pdf">edgeR_DifferentialCounts_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
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661 <tr class="odd_row"><td><a href="edgeR_DifferentialCounts_MDSplot.pdf">edgeR_DifferentialCounts_MDSplot.pdf</a></td><td>5.0 KB</td></tr>
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662 <tr><td><a href="edgeR_DifferentialCounts_qqplot.pdf">edgeR_DifferentialCounts_qqplot.pdf</a></td><td>15.2 KB</td></tr>
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663 <tr class="odd_row"><td><a href="edgeR_DifferentialCounts_raw_norm_counts_box.pdf">edgeR_DifferentialCounts_raw_norm_counts_box.pdf</a></td><td>7.8 KB</td></tr>
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664 <tr><td><a href="edgeR_DifferentialCounts_smearplot.pdf">edgeR_DifferentialCounts_smearplot.pdf</a></td><td>16.6 KB</td></tr>
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665 <tr class="odd_row"><td><a href="edgeR_DifferentialCounts_top_100_heatmap.pdf">edgeR_DifferentialCounts_top_100_heatmap.pdf</a></td><td>11.5 KB</td></tr>
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666 <tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr>
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667 </table></div><br/>
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668 </div></body></html>
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