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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 "DifferentialCounts" run at 07/08/2013 15:46:55</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_MA_plot.pdf"><img src="DESeq2_MA_plot.png" title="Click to download a PDF of DESeq2_MA_plot.pdf" hspace="5" width="400"
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17 alt="Image called DESeq2_MA_plot.pdf"/></a></td>
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18
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19 <td><a href="DESeq2_PCA_plot.pdf"><img src="DESeq2_PCA_plot.png" title="Click to download a PDF of DESeq2_PCA_plot.pdf" hspace="5" width="400"
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20 alt="Image called DESeq2_PCA_plot.pdf"/></a></td>
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21
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22 <td><a href="DESeq2_dispersion_estimates.pdf"><img src="DESeq2_dispersion_estimates.png" title="Click to download a PDF of DESeq2_dispersion_estimates.pdf" hspace="5" width="400"
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23 alt="Image called DESeq2_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_qqplot.pdf"><img src="DESeq2_qqplot.png" title="Click to download a PDF of DESeq2_qqplot.pdf" hspace="5" width="400"
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27 alt="Image called DESeq2_qqplot.pdf"/></a></td>
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28
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29 <td><a href="DESeq2_sample_distance_plot.pdf"><img src="DESeq2_sample_distance_plot.png" title="Click to download a PDF of DESeq2_sample_distance_plot.pdf" hspace="5" width="400"
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30 alt="Image called DESeq2_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 pvalue padj NReads URL
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42
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43 Mir192 Mir192 271352.97636 6.965264 0.2150593 4.096936e-230 4.576278e-227 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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44
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45 Mir122a Mir122a 10112.31117 10.312083 0.3292695 2.649323e-215 1.479647e-212 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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46
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47 Mir149 Mir149 810.35429 -6.911118 0.2341392 1.735537e-191 6.461982e-189 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 -3.104086 0.1191688 1.424246e-149 3.977206e-147 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 Mir181d Mir181d 275.22797 -3.581172 0.1778187 3.329371e-90 7.437816e-88 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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52
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53 Mir204 Mir204 347.57397 -7.284200 0.3771119 3.959336e-83 7.370965e-81 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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54
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55 Mir23b Mir23b 2028.55377 -2.065110 0.1085802 1.182361e-80 1.886711e-78 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
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56
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57 Mir27a Mir27a 2788.72629 -3.016676 0.1688167 2.036708e-71 2.843754e-69 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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58
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59 Mir195 Mir195 519.86200 -3.152795 0.1784796 7.838123e-70 9.727982e-68 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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60
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61 Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 1.013490e-63 1.132068e-61 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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62
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63 Mir208b Mir208b 1649.77924 -11.396172 0.6771238 1.464479e-63 1.487112e-61 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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64
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65 Mir10b Mir10b 27820.40551 -5.071453 0.3044889 2.754493e-62 2.563974e-60 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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66
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67 Mir181c Mir181c 2765.96510 -3.660964 0.2275711 3.141153e-58 2.698975e-56 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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68
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69 Mir208a Mir208a 616.76981 -10.356524 0.6559217 3.688385e-56 2.942804e-54 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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70
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71 Mir490 Mir490 220.99790 -8.059660 0.5142876 2.369067e-55 1.764165e-53 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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72
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73 Mir203 Mir203 772.92882 1.990849 0.1274099 4.877239e-55 3.404923e-53 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
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74
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75 Mir215 Mir215 152.78082 -3.004380 0.1939090 3.822339e-54 2.511502e-52 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
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76
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77 Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 9.922020e-52 6.157165e-50 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
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78
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79 Mir214 Mir214 134.69038 -3.216444 0.2154916 2.230148e-50 1.311093e-48 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
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80
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81 Mir21 Mir21 26121.31011 2.963903 0.2008617 2.817434e-49 1.573537e-47 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
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82
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83 Mir1948 Mir1948 263.89527 7.074045 0.4867225 7.374030e-48 3.922282e-46 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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84
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85 Mir27b Mir27b 76478.05753 -1.904653 0.1312889 1.088626e-47 5.527251e-46 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
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86
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87 Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 1.134862e-45 5.511484e-44 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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88
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89 Mir499 Mir499 712.45950 -10.577061 0.7528467 7.766408e-45 3.614616e-43 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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90
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91 Mir101b Mir101b 6846.19683 3.791681 0.2809666 1.670548e-41 7.464007e-40 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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92
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93 Mir132 Mir132 106.46062 -2.797928 0.2083376 4.046163e-41 1.738294e-39 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
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94
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95 Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 6.764675e-38 2.798571e-36 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 -2.170303 0.1696199 1.746403e-37 6.966899e-36 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 Mir155 Mir155 57.66182 -3.788079 0.3056585 2.845488e-35 1.096004e-33 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
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100
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101 Mir322 Mir322 899.53469 -3.126011 0.2622595 9.363374e-33 3.486296e-31 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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102
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103 Mir378 Mir378 483.21548 -2.994300 0.2577321 3.343457e-31 1.204723e-29 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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104
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105 Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 1.491830e-30 5.049617e-29 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 -2.712674 0.2361028 1.491830e-30 5.049617e-29 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 Mir199b Mir199b 47.84725 -5.294373 0.4644474 4.215162e-30 1.384805e-28 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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110
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111 Mir802 Mir802 166.83414 8.816580 0.7782636 9.478527e-30 3.025004e-28 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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112
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113 Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 1.324797e-28 4.110551e-27 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
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114
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115 Mir301 Mir301 260.53406 -1.676984 0.1526772 4.570133e-28 1.379686e-26 2119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a>
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116
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117 Snord104 Snord104 3851.90119 2.386573 0.2173857 4.847914e-28 1.425032e-26 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
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118
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119 Mir150 Mir150 553.20599 -2.836881 0.2595088 8.127991e-28 2.327940e-26 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
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120
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121 Mir148a Mir148a 118994.46955 2.678852 0.2481801 3.675045e-27 1.026256e-25 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
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122
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123 5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 8.101331e-26 2.207119e-24 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
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124
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125 Mir193 Mir193 45.70861 4.991530 0.4814098 3.446492e-25 9.166027e-24 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
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126
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127 Mir3073 Mir3073 98.93199 8.208709 0.7944742 5.036320e-25 1.308272e-23 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
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128
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129 Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 8.355633e-25 2.121191e-23 609 <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 -3.023491 0.2948614 1.136165e-24 2.820214e-23 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
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132
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133 Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 9.923707e-23 2.409735e-21 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
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134
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135 Mir184 Mir184 32.23796 -4.865023 0.4962776 1.092606e-22 2.596683e-21 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
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136
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137 Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 4.826269e-22 1.123113e-20 352 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a>
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138
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139 Snord91a Snord91a 168.95251 2.700421 0.2835464 1.670595e-21 3.808275e-20 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
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140
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141 Mir200b Mir200b 87.13638 5.940702 0.6338554 7.094881e-21 1.584996e-19 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</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 Loading required package: gtools
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151
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152 Loading required package: gdata
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153
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154 gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
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155
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156 gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
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157
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158 Attaching package: ‘gdata’
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159
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160 The following object is masked from ‘package:stats’:
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161
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162 nobs
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163
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164 The following object is masked from ‘package:utils’:
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165
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166 object.size
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167
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168 Loading required package: caTools
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169
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170 Loading required package: grid
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171
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172 Loading required package: KernSmooth
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173
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174 KernSmooth 2.23 loaded
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175
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176 Copyright M. P. Wand 1997-2009
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177
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178 Loading required package: MASS
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179
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180 Attaching package: ‘gplots’
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181
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182 The following object is masked from ‘package:stats’:
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183
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184 lowess
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185
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186 Loading required package: methods
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187
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188 Loading required package: limma
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189
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190 Loading required package: splines
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191
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192 Loading required package: DESeq2
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193
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194 Loading required package: GenomicRanges
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195
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196 Loading required package: BiocGenerics
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197
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198 Loading required package: parallel
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199
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200 Attaching package: ‘BiocGenerics’
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201
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202 The following object is masked from ‘package:parallel’:
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203
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204 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
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205
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206 The following object is masked from ‘package:gdata’:
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207
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208 combine
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209
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210 The following object is masked from ‘package:stats’:
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211
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212 xtabs
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213
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214 The following object is masked from ‘package:base’:
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215
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216 anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, 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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217
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218 Loading required package: IRanges
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219
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220 Attaching package: ‘IRanges’
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221
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222 The following object is masked from ‘package:gplots’:
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223
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224 space
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225
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226 The following object is masked from ‘package:caTools’:
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227
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228 runmean
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229
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230 The following object is masked from ‘package:gdata’:
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231
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232 trim
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233
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234 Loading required package: Biobase
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235
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236 Welcome to Bioconductor
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237
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238 Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
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239
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240 Loading required package: lattice
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241
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242 Loading required package: Rcpp
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243
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244 Loading required package: RcppArmadillo
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245
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246 Attaching package: ‘DESeq2’
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247
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248 The following object is masked from ‘package:limma’:
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249
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250 plotMA
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251
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252 gene-wise dispersion estimates
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253
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254 mean-dispersion relationship
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255
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256 final dispersion estimates
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257
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258 you had estimated dispersions, replacing these
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259
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260 gene-wise dispersion estimates
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261
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262 mean-dispersion relationship
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263
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264 final dispersion estimates
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265
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266 you had estimated dispersions, replacing these
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267
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268 gene-wise dispersion estimates
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269
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270 mean-dispersion relationship
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271
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272 final dispersion estimates
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273
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274 Warning messages:
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275
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276 1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == :
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277
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278 Outlier (-Inf) in boxplot 1 is not drawn
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279
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280 2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == :
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281
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282 Outlier (-Inf) in boxplot 3 is not drawn
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283
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284 3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067, :
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285
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286 some notches went outside hinges ('box'): maybe set notch=FALSE
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287
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288 4: In par(defpar) : calling par(new=TRUE) with no plot
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289
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290
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291 </pre>
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292
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293 <div class="toolFormTitle">VOOM images and outputs</div>
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294 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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295 <div><table class="simple" cellpadding="2" cellspacing="2">
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296 <tr>
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297 <td><a href="VOOM_mean_variance_plot.pdf"><img src="VOOM_mean_variance_plot.png" title="Click to download a PDF of VOOM_mean_variance_plot.pdf" hspace="5" width="400"
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298 alt="Image called VOOM_mean_variance_plot.pdf"/></a></td>
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299
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300 <td><a href="VOOM_qqplot.pdf"><img src="VOOM_qqplot.png" title="Click to download a PDF of VOOM_qqplot.pdf" hspace="5" width="400"
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301 alt="Image called VOOM_qqplot.pdf"/></a></td>
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302 </tr>
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303
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304 </table></div>
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305
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306 <div class="toolFormTitle">VOOM log output</div>
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307
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308 <pre>
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309
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310 # VOOM top 50
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311
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312 ID logFC AveExpr t P.Value adj.P.Val B NReads URL
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313
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314 Mir192 Mir192 6.948883 14.6763803 42.722954 2.301199e-16 2.625668e-13 27.266471 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
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315
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316 Mir208a Mir208a -11.015018 3.9395538 -23.252407 1.118938e-12 6.383542e-10 17.208662 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
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317
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318 Mir122a Mir122a 10.426125 8.1698641 21.722912 2.859682e-12 1.087633e-09 17.760171 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
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319
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320 Mir149 Mir149 -7.030463 6.3160807 -20.883835 4.915491e-12 1.402144e-09 17.277609 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
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321
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322 Mir208b Mir208b -12.433228 4.6076218 -19.592458 1.179199e-11 2.690931e-09 15.683666 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
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323
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324 Mir10b Mir10b -5.130915 12.2628672 -18.242023 3.124991e-11 4.963978e-09 16.221503 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
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325
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326 Mir143hg Mir143hg -2.249221 16.2444825 -18.082481 3.521739e-11 4.963978e-09 16.026695 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
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327
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328 Mir143 Mir143 -2.251067 16.2358599 -18.081481 3.524391e-11 4.963978e-09 16.026084 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
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329
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330 Mir499 Mir499 -11.567529 3.7874598 -17.942086 3.915496e-11 4.963978e-09 14.821741 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
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331
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332 Mir802 Mir802 9.158434 2.9157675 17.316522 6.338616e-11 7.232360e-09 14.381577 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
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333
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334 Mir3073 Mir3073 8.420542 2.5457189 16.702657 1.033066e-10 1.036045e-08 13.985845 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
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335
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336 Mir148a Mir148a 2.638213 15.4435820 16.548188 1.171186e-10 1.036045e-08 14.814792 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
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337
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338 Mir101b Mir101b 3.765722 10.8508440 16.538566 1.180419e-10 1.036045e-08 14.900027 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
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339
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340 Mir490 Mir490 -8.474378 3.7506957 -16.259650 1.484816e-10 1.210125e-08 13.424617 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
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341
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342 Mir21 Mir21 2.938537 13.1642917 15.375404 3.148335e-10 2.394833e-08 13.867698 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
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343
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344 Mir181c Mir181c -3.742560 9.6295577 -15.242361 3.537063e-10 2.522368e-08 13.810405 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
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345
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346 Mir204 Mir204 -7.684425 4.7751735 -15.033484 4.254268e-10 2.855364e-08 12.822427 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
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347
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348 Mir23a Mir23a -3.165768 8.7896592 -14.631179 6.110682e-10 3.873493e-08 13.269174 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
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349
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350 Mir181d Mir181d -3.636211 6.3713218 -14.317073 8.157508e-10 4.898798e-08 12.956333 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
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351
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352 Mir133b Mir133b -6.493549 1.2544862 -13.969968 1.129934e-09 6.446275e-08 11.982684 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
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353
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354 Mir27a Mir27a -3.106935 9.9255796 -13.838251 1.281011e-09 6.960160e-08 12.513086 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
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355
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356 Mir194-2 Mir194-2 5.264136 6.0897615 13.044012 2.792884e-09 1.448491e-07 11.715753 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
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357
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358 Mir195 Mir195 -3.216595 7.4509350 -12.869478 3.332788e-09 1.653353e-07 11.587523 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
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359
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360 Mir27b Mir27b -1.976376 15.0957731 -11.756036 1.082197e-08 5.144946e-07 10.127719 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
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361
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362 Mir378 Mir378 -3.097393 7.3832049 -11.684163 1.171371e-08 5.346138e-07 10.329692 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
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363
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364 Snord104 Snord104 2.337374 10.6109024 11.495675 1.444482e-08 6.339052e-07 10.023395 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
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365
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366 Mir1983 Mir1983 -5.895500 0.9931851 -11.445812 1.527548e-08 6.441605e-07 9.749260 101 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
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367
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368 Mir322 Mir322 -3.296618 8.2153415 -11.415362 1.580762e-08 6.441605e-07 10.008472 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
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369
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370 Mir200a Mir200a 6.191561 1.7981309 11.322172 1.756229e-08 6.909853e-07 9.662295 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
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371
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372 Mir215 Mir215 -3.045873 5.7544234 -11.148134 2.141822e-08 8.082459e-07 9.753268 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
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373
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374 Dnm3os Dnm3os -3.363344 5.8607432 -11.092261 2.283960e-08 8.082459e-07 9.689496 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
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375
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376 Mir182 Mir182 4.903995 7.1511683 11.074468 2.331304e-08 8.082459e-07 9.658842 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
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377
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378 Mir181a-2 Mir181a-2 -3.048298 6.9414651 -11.072128 2.337609e-08 8.082459e-07 9.644017 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
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379
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380 Mir1948 Mir1948 7.195525 4.5513493 11.005492 2.524936e-08 8.473388e-07 9.341794 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
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381
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382 Mir214 Mir214 -3.280874 5.4784451 -10.768257 3.332555e-08 1.086413e-06 9.318504 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
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383
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384 Mir153 Mir153 -5.963803 1.4386315 -10.727082 3.498742e-08 1.093990e-06 9.035569 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
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385
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386 Cyp3a25 Cyp3a25 6.318200 1.4888933 10.698226 3.620443e-08 1.093990e-06 9.024973 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
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387
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388 Gm5441 Gm5441 -5.982176 1.4484953 -10.692891 3.643436e-08 1.093990e-06 9.000362 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
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389
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390 Mir125b-2 Mir125b-2 -3.077678 7.4316058 -10.446668 4.893073e-08 1.431538e-06 8.884250 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
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391
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392 Mir133a-1 Mir133a-1 -5.144671 0.5903264 -10.358205 5.447229e-08 1.553822e-06 8.575535 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
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393
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394 1110038B12Rik 1110038B12Rik 2.226702 10.8487089 10.194609 6.655312e-08 1.852125e-06 8.439308 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
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395
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396 Mir132 Mir132 -2.847559 5.3211839 -10.110952 7.380297e-08 2.004981e-06 8.531491 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
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397
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398 Rabggtb Rabggtb 1.935779 9.9874171 9.928995 9.262821e-08 2.457879e-06 8.133384 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
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399
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400 Mir504 Mir504 -5.256127 0.6221088 -9.892894 9.693595e-08 2.513725e-06 8.068853 69 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
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|
401
|
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402 Mir150 Mir150 -2.938531 7.6297870 -9.842102 1.033602e-07 2.620755e-06 8.116464 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
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403
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404 Mir199b Mir199b -5.752816 2.8805143 -9.823920 1.057683e-07 2.623514e-06 7.979387 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
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405
|
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406 Mir23b Mir23b -2.124129 9.8141190 -9.806316 1.081569e-07 2.625681e-06 7.979464 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
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407
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408 Mir24-2 Mir24-2 -2.833979 7.3083691 -9.767192 1.136724e-07 2.646944e-06 8.030550 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
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409
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410 Mir3074-2 Mir3074-2 -2.833979 7.3083691 -9.767192 1.136724e-07 2.646944e-06 8.030550 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
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411
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412 Mir155 Mir155 -3.906600 3.9899000 -9.732173 1.188627e-07 2.712448e-06 8.046518 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
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413
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414
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415 </pre>
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416
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417 <div class="toolFormTitle">edgeR images and outputs</div>
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418 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
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419 <div><table class="simple" cellpadding="2" cellspacing="2">
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420 <tr>
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421 <td><a href="edgeR_BCV_vs_abundance.pdf"><img src="edgeR_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_BCV_vs_abundance.pdf" hspace="5" width="400"
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422 alt="Image called edgeR_BCV_vs_abundance.pdf"/></a></td>
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423
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424 <td><a href="edgeR_GoodnessofFit.pdf"><img src="edgeR_GoodnessofFit.png" title="Click to download a PDF of edgeR_GoodnessofFit.pdf" hspace="5" width="400"
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425 alt="Image called edgeR_GoodnessofFit.pdf"/></a></td>
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426
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427 <td><a href="edgeR_MDSplot.pdf"><img src="edgeR_MDSplot.png" title="Click to download a PDF of edgeR_MDSplot.pdf" hspace="5" width="400"
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428 alt="Image called edgeR_MDSplot.pdf"/></a></td>
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429 </tr>
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430 <tr>
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431 <td><a href="edgeR_qqplot.pdf"><img src="edgeR_qqplot.png" title="Click to download a PDF of edgeR_qqplot.pdf" hspace="5" width="400"
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432 alt="Image called edgeR_qqplot.pdf"/></a></td>
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433
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434 <td><a href="edgeR_raw_norm_counts_box.pdf"><img src="edgeR_raw_norm_counts_box.png" title="Click to download a PDF of edgeR_raw_norm_counts_box.pdf" hspace="5" width="400"
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435 alt="Image called edgeR_raw_norm_counts_box.pdf"/></a></td>
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436
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437 <td><a href="edgeR_smearplot.pdf"><img src="edgeR_smearplot.png" title="Click to download a PDF of edgeR_smearplot.pdf" hspace="5" width="400"
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438 alt="Image called edgeR_smearplot.pdf"/></a></td>
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439 </tr>
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440 <tr>
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441 <td><a href="edgeR_top_100_heatmap.pdf"><img src="edgeR_top_100_heatmap.png" title="Click to download a PDF of edgeR_top_100_heatmap.pdf" hspace="5" width="400"
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442 alt="Image called edgeR_top_100_heatmap.pdf"/></a></td>
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443
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444 <td> </td><td> </td>
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445 </tr></table></div>
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446
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447 <div class="toolFormTitle">edgeR log output</div>
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448
|
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449 <pre>
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450
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451 [1] prior.df = 8
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452
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453 [1] "No GLM fit outlier genes found\n"
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454
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455 [1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333
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456
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457 [1] heart liver
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458
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459 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
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460
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461 [1] raw contig counts by sample:
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462
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463 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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464
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465 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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466
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467 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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468
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469 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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470
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471 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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472
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473 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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474
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475 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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476
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477 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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478
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479 [1] normalised contig counts by sample:
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480
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481 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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482
|
|
|
483 Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf
|
|
|
484
|
|
|
485 1st Qu.: 0 1st Qu.:-Inf 1st Qu.: 0 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf
|
|
|
486
|
|
|
487 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0
|
|
|
488
|
|
|
489 Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf
|
|
|
490
|
|
|
491 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1
|
|
|
492
|
|
|
493 Max. : 6 Max. : 6 Max. : 6 Max. : 5 Max. : 5 Max. : 5 Max. : 6 Max. : 5
|
|
|
494
|
|
|
495 [1] Using ncol rawrs= 8
|
|
|
496
|
|
|
497 [1] # edgeR Top tags\n
|
|
|
498
|
|
|
499 Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL
|
|
|
500
|
|
|
501 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>
|
|
|
502
|
|
|
503 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>
|
|
|
504
|
|
|
505 Mir208b Mir208b -13.291635 9.905945 417.69758 7.737463e-93 2.942815e-90 0.10508096 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
|
|
|
506
|
|
|
507 Mir122a Mir122a 10.514683 12.478088 415.17429 2.740525e-92 7.817349e-90 0.10803882 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
|
|
|
508
|
|
|
509 Mir204 Mir204 -7.498162 7.634507 341.30678 3.313430e-76 7.561247e-74 0.06907958 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
|
|
|
510
|
|
|
511 Mir499 Mir499 -13.577454 8.700078 325.79199 7.930755e-73 1.508165e-70 0.12042284 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
|
|
|
512
|
|
|
513 Mir490 Mir490 -8.534394 6.991023 303.17184 6.710366e-68 1.093790e-65 0.07949711 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
|
|
|
514
|
|
|
515 Mir192 Mir192 6.953853 17.169364 217.22867 3.638307e-49 5.189135e-47 0.12700995 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
|
|
|
516
|
|
|
517 Mir802 Mir802 11.440805 6.593380 212.88059 3.231644e-48 4.097007e-46 0.12273671 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
|
|
|
518
|
|
|
519 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>
|
|
|
520
|
|
|
521 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>
|
|
|
522
|
|
|
523 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>
|
|
|
524
|
|
|
525 Mir181c Mir181c -3.767686 10.639598 169.87390 7.883295e-39 6.919107e-37 0.06368883 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
|
|
|
526
|
|
|
527 Mir3073 Mir3073 10.686337 5.859950 164.86740 9.778593e-38 7.969554e-36 0.14069249 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
|
|
|
528
|
|
|
529 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>
|
|
|
530
|
|
|
531 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>
|
|
|
532
|
|
|
533 Mir10b Mir10b -5.182616 13.946466 147.24793 6.926819e-34 4.649118e-32 0.12268790 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
|
|
|
534
|
|
|
535 Mir101b Mir101b 3.759962 11.863187 136.31359 1.703812e-31 1.080028e-29 0.07961343 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
|
|
|
536
|
|
|
537 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>
|
|
|
538
|
|
|
539 Mir27a Mir27a -3.064687 10.642480 124.98911 5.117477e-29 2.919520e-27 0.06113852 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
|
|
|
540
|
|
|
541 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>
|
|
|
542
|
|
|
543 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>
|
|
|
544
|
|
|
545 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>
|
|
|
546
|
|
|
547 Mir181a-2 Mir181a-2 -3.000177 7.637692 101.38361 7.578821e-24 3.603098e-22 0.06896654 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
|
|
|
548
|
|
|
549 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>
|
|
|
550
|
|
|
551 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>
|
|
|
552
|
|
|
553 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>
|
|
|
554
|
|
|
555 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>
|
|
|
556
|
|
|
557 Mir133b Mir133b -8.383611 3.584760 83.96681 5.031517e-20 1.960318e-18 0.17482280 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
|
|
|
558
|
|
|
559 Mir150 Mir150 -2.883446 8.307765 83.91918 5.154210e-20 1.960318e-18 0.08008123 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
|
|
|
560
|
|
|
561 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>
|
|
|
562
|
|
|
563 Mir24-2 Mir24-2 -2.778307 7.935651 83.71222 5.723024e-20 2.040616e-18 0.07427992 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
|
|
|
564
|
|
|
565 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>
|
|
|
566
|
|
|
567 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>
|
|
|
568
|
|
|
569 Mir214 Mir214 -3.271172 6.271755 80.43948 2.997458e-19 9.771712e-18 0.09566584 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
|
|
|
570
|
|
|
571 Snord104 Snord104 2.330488 11.053611 79.50529 4.809369e-19 1.524303e-17 0.05915990 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
|
|
|
572
|
|
|
573 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>
|
|
|
574
|
|
|
575 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>
|
|
|
576
|
|
|
577 Mir21 Mir21 2.923147 13.825255 75.51798 3.620938e-18 1.059357e-16 0.09395834 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
|
|
|
578
|
|
|
579 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>
|
|
|
580
|
|
|
581 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>
|
|
|
582
|
|
|
583 Cyp3a25 Cyp3a25 8.681501 3.972085 72.29680 1.851471e-17 5.029829e-16 0.23125383 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
|
|
|
584
|
|
|
585 Rabggtb Rabggtb 1.934093 10.298211 72.02043 2.129809e-17 5.651422e-16 0.04596646 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
|
|
|
586
|
|
|
587 Mir23b Mir23b -2.100584 10.184110 71.44225 2.854935e-17 7.403367e-16 0.05416378 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
|
|
|
588
|
|
|
589 Snord52 Snord52 2.207491 10.217554 71.27974 3.100027e-17 7.860292e-16 0.05941483 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
|
|
|
590
|
|
|
591 Gm5441 Gm5441 -6.881248 3.538457 70.05615 5.764004e-17 1.429724e-15 0.20097284 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
|
|
|
592
|
|
|
593 Mir153 Mir153 -6.857671 3.517446 69.37600 8.137282e-17 1.975455e-15 0.20158808 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
|
|
|
594
|
|
|
595 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>
|
|
|
596
|
|
|
597 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>
|
|
|
598
|
|
|
599 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>
|
|
|
600
|
|
|
601 [1] # 416 tags significant at adj p= 0.05
|
|
|
602
|
|
|
603
|
|
|
604 </pre>
|
|
|
605
|
|
|
606 <div class="toolFormTitle">Other images and outputs</div>
|
|
|
607 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
|
|
|
608 <div><table class="simple" cellpadding="2" cellspacing="2">
|
|
|
609 <tr>
|
|
|
610 <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"
|
|
|
611 alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td>
|
|
|
612
|
|
|
613 <td><a href="Venn_significant_genes_overlap.pdf"><img src="Venn_significant_genes_overlap.png" title="Click to download a PDF of Venn_significant_genes_overlap.pdf" hspace="5" width="400"
|
|
|
614 alt="Image called Venn_significant_genes_overlap.pdf"/></a></td>
|
|
|
615 </tr>
|
|
|
616 <tr>
|
|
|
617 <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"
|
|
|
618 alt="Image called sample_counts_histogram.pdf"/></a></td>
|
|
|
619
|
|
|
620 <td> </td>
|
|
|
621 </tr></table></div>
|
|
|
622
|
|
|
623 <div class="toolFormTitle">Other log output</div>
|
|
|
624
|
|
|
625 <pre>
|
|
|
626
|
|
|
627 ## Toolfactory generated command line = Rscript - None None
|
|
|
628
|
|
|
629 Got TCols=1 5 6 7; CCols=2 3 4 8
|
|
|
630
|
|
|
631 [1] # Quantiles for non-zero row counts:
|
|
|
632
|
|
|
633 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
|
|
|
634
|
|
|
635 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0
|
|
|
636
|
|
|
637 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
|
|
|
638
|
|
|
639 [1] "@@ using genecards substitution for urls"
|
|
|
640
|
|
|
641 [1] # urls
|
|
|
642
|
|
|
643 [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>
|
|
|
644
|
|
|
645 [6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
|
|
|
646
|
|
|
647 [1] # Total low count contigs per sample = 170,67,203,86,145,111,155,120
|
|
|
648
|
|
|
649 [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
|
|
|
650
|
|
|
651 [1] Using design matrix:
|
|
|
652
|
|
|
653 (Intercept) groupliver
|
|
|
654
|
|
|
655 1 1 1
|
|
|
656
|
|
|
657 2 1 1
|
|
|
658
|
|
|
659 3 1 1
|
|
|
660
|
|
|
661 4 1 1
|
|
|
662
|
|
|
663 5 1 0
|
|
|
664
|
|
|
665 6 1 0
|
|
|
666
|
|
|
667 7 1 0
|
|
|
668
|
|
|
669 8 1 0
|
|
|
670
|
|
|
671 attr(,"assign")
|
|
|
672
|
|
|
673 [1] 0 1
|
|
|
674
|
|
|
675 attr(,"contrasts")
|
|
|
676
|
|
|
677 attr(,"contrasts")$group
|
|
|
678
|
|
|
679 [1] contr.treatment
|
|
|
680
|
|
|
681 R version 3.0.1 (2013-05-16)
|
|
|
682
|
|
|
683 Platform: x86_64-unknown-linux-gnu (64-bit)
|
|
|
684
|
|
|
685 locale:
|
|
|
686
|
|
|
687 [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=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
|
|
|
688
|
|
|
689 attached base packages:
|
|
|
690
|
|
|
691 [1] parallel splines methods grid stats graphics grDevices utils datasets base
|
|
|
692
|
|
|
693 other attached packages:
|
|
|
694
|
|
|
695 [1] RColorBrewer_1.0-5 DESeq2_1.0.18 RcppArmadillo_0.3.900.7 Rcpp_0.10.4 lattice_0.20-15 Biobase_2.20.1 GenomicRanges_1.12.4 IRanges_1.18.2 BiocGenerics_0.6.0 edgeR_3.2.4 limma_3.16.7 gplots_2.11.3 MASS_7.3-28 KernSmooth_2.23-10 caTools_1.14 gdata_2.13.2 gtools_3.0.0 stringr_0.6.2
|
|
|
696
|
|
|
697 loaded via a namespace (and not attached):
|
|
|
698
|
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699 [1] annotate_1.38.0 AnnotationDbi_1.22.6 bitops_1.0-5 DBI_0.2-7 genefilter_1.42.0 locfit_1.5-9.1 RSQLite_0.11.4 stats4_3.0.1 survival_2.37-4 XML_3.98-1.1 xtable_1.7-1
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700
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701
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702 </pre>
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703
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704 <div class="toolFormTitle">All output files available for downloading</div>
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705
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706 <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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707
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708 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.0 KB</td></tr>
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709 <tr class="odd_row"><td><a href="DESeq2_MA_plot.pdf">DESeq2_MA_plot.pdf</a></td><td>14.7 KB</td></tr>
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710 <tr><td><a href="DESeq2_PCA_plot.pdf">DESeq2_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
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711 <tr class="odd_row"><td><a href="DESeq2_dispersion_estimates.pdf">DESeq2_dispersion_estimates.pdf</a></td><td>188.4 KB</td></tr>
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712 <tr><td><a href="DESeq2_qqplot.pdf">DESeq2_qqplot.pdf</a></td><td>14.4 KB</td></tr>
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713 <tr class="odd_row"><td><a href="DESeq2_sample_distance_plot.pdf">DESeq2_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>
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714 <tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>27.1 KB</td></tr>
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715 <tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>3.1 KB</td></tr>
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716 <tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.2 KB</td></tr>
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717 <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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718 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>
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719 <tr class="odd_row"><td><a href="VOOM_mean_variance_plot.pdf">VOOM_mean_variance_plot.pdf</a></td><td>16.7 KB</td></tr>
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720 <tr><td><a href="VOOM_qqplot.pdf">VOOM_qqplot.pdf</a></td><td>17.6 KB</td></tr>
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721 <tr class="odd_row"><td><a href="Venn_significant_genes_overlap.pdf">Venn_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>
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722 <tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr>
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723 <tr class="odd_row"><td><a href="edgeR_BCV_vs_abundance.pdf">edgeR_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
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724 <tr><td><a href="edgeR_GoodnessofFit.pdf">edgeR_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
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725 <tr class="odd_row"><td><a href="edgeR_MDSplot.pdf">edgeR_MDSplot.pdf</a></td><td>4.9 KB</td></tr>
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726 <tr><td><a href="edgeR_qqplot.pdf">edgeR_qqplot.pdf</a></td><td>15.2 KB</td></tr>
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727 <tr class="odd_row"><td><a href="edgeR_raw_norm_counts_box.pdf">edgeR_raw_norm_counts_box.pdf</a></td><td>7.8 KB</td></tr>
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728 <tr><td><a href="edgeR_smearplot.pdf">edgeR_smearplot.pdf</a></td><td>16.6 KB</td></tr>
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729 <tr class="odd_row"><td><a href="edgeR_top_100_heatmap.pdf">edgeR_top_100_heatmap.pdf</a></td><td>11.3 KB</td></tr>
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730 <tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr>
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731 </table></div><br/>
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732 </div></body></html>
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733
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