Mercurial > repos > fubar > differential_count_models

comparison test-data/edgeRtest1out.html @ 130:a9ffdf5f7d2a draft

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author fubar
date Thu, 01 Jan 2015 21:53:07 -0500
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129:a95f5496d330 130:a9ffdf5f7d2a
6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
7 </head> 7 </head>
8 <body> 8 <body>
9 <div class="toolFormBody"> 9 <div class="toolFormBody">
10 10
11 <div class="infomessage">Galaxy Tool "DifferentialCounts" run at 06/10/2014 15:33:02</div><br/> 11 <div class="infomessage">Galaxy Tool "Differential_Counts" run at 28/12/2014 21:02:37</div><br/>
12 <div class="toolFormTitle">DESeq2 images and outputs</div> 12 <div class="toolFormTitle">DESeq2 images and outputs</div>
13 (Click on a thumbnail image to download the corresponding original PDF image)<br/> 13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
14 <div><table class="simple" cellpadding="2" cellspacing="2"> 14 <div><table class="simple" cellpadding="2" cellspacing="2">
15 <tr> 15 <tr>
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" 16 <td><a href="DESeq2_edgeRtest_MA_plot.pdf"><img src="DESeq2_edgeRtest_MA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_MA_plot.pdf" hspace="5" width="400"
17 alt="Image called DESeq2_DifferentialCounts_MA_plot.pdf"/></a></td> 17 alt="Image called DESeq2_edgeRtest_MA_plot.pdf"/></a></td>
18 18
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" 19 <td><a href="DESeq2_edgeRtest_PCA_plot.pdf"><img src="DESeq2_edgeRtest_PCA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_PCA_plot.pdf" hspace="5" width="400"
20 alt="Image called DESeq2_DifferentialCounts_PCA_plot.pdf"/></a></td> 20 alt="Image called DESeq2_edgeRtest_PCA_plot.pdf"/></a></td>
21 21
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" 22 <td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf"><img src="DESeq2_edgeRtest_dispersion_estimates.png" title="Click to download a PDF of DESeq2_edgeRtest_dispersion_estimates.pdf" hspace="5" width="400"
23 alt="Image called DESeq2_DifferentialCounts_dispersion_estimates.pdf"/></a></td> 23 alt="Image called DESeq2_edgeRtest_dispersion_estimates.pdf"/></a></td>
24 </tr> 24 </tr>
25 <tr> 25 <tr>
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" 26 <td><a href="DESeq2_edgeRtest_qqplot.pdf"><img src="DESeq2_edgeRtest_qqplot.png" title="Click to download a PDF of DESeq2_edgeRtest_qqplot.pdf" hspace="5" width="400"
27 alt="Image called DESeq2_DifferentialCounts_qqplot.pdf"/></a></td> 27 alt="Image called DESeq2_edgeRtest_qqplot.pdf"/></a></td>
28 28
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" 29 <td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf"><img src="DESeq2_edgeRtest_sample_distance_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_sample_distance_plot.pdf" hspace="5" width="400"
30 alt="Image called DESeq2_DifferentialCounts_sample_distance_plot.pdf"/></a></td> 30 alt="Image called DESeq2_edgeRtest_sample_distance_plot.pdf"/></a></td>
31 31
32 <td>&nbsp;</td> 32 <td>&nbsp;</td>
33 </tr></table></div> 33 </tr></table></div>
34 34
35 <div class="toolFormTitle">DESeq2 log output</div> 35 <div class="toolFormTitle">DESeq2 log output</div>
38 38
39 # DESeq top 50 39 # DESeq top 50
40 40
41 Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL 41 Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL
42 42
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> 43 Mir192 Mir192 271352.97636 6.965264 0.2150593 32.387646 4.096935e-230 3.818343e-227 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
44 44
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> 45 Mir122a Mir122a 10112.31117 10.312083 0.3292695 31.318061 2.649329e-215 1.234587e-212 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
46 46
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> 47 Mir149 Mir149 810.35429 -6.911118 0.2341392 -29.517132 1.735536e-191 5.391733e-189 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
48 48
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> 49 Mir23a Mir23a 1289.18043 -3.104086 0.1191688 -26.047815 1.424245e-149 3.318491e-147 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
50 50
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> 51 Mir181d Mir181d 275.22797 -3.581172 0.1778187 -20.139461 3.329373e-90 6.205952e-88 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
52 52
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> 53 Mir204 Mir204 347.57397 -7.284200 0.3771119 -19.315751 3.959346e-83 6.150183e-81 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
54 54
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> 55 Mir23b Mir23b 2028.55377 -2.065110 0.1085802 -19.019217 1.182361e-80 1.574229e-78 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
56 56
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> 57 Mir27a Mir27a 2788.72629 -3.016676 0.1688167 -17.869539 2.036708e-71 2.372765e-69 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
58 58
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> 59 Mir195 Mir195 519.86200 -3.152795 0.1784796 -17.664734 7.838131e-70 8.116820e-68 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
60 60
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> 61 Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 16.852045 1.013492e-63 9.445744e-62 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
62 62
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> 63 Mir208b Mir208b 1649.77924 -11.396172 0.6771238 -16.830264 1.464482e-63 1.240816e-61 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
64 64
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> 65 Mir10b Mir10b 27820.40551 -5.071453 0.3044884 -16.655656 2.753110e-62 2.138249e-60 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
66 66
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> 67 Mir181c Mir181c 2765.96510 -3.660964 0.2275711 -16.087120 3.141152e-58 2.251965e-56 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
68 68
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> 69 Mir208a Mir208a 616.76981 -10.356524 0.6559218 -15.789267 3.688391e-56 2.455415e-54 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
70 70
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> 71 Mir490 Mir490 220.99790 -8.059660 0.5142876 -15.671504 2.369067e-55 1.471980e-53 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
72 72
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> 73 Mir203 Mir203 772.92882 1.990849 0.1274099 15.625546 4.877239e-55 2.840992e-53 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
74 74
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> 75 Mir215 Mir215 152.78082 -3.004380 0.1939090 -15.493765 3.822341e-54 2.095542e-52 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
76 76
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> 77 Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 -15.132265 9.922045e-52 5.137415e-50 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
78 78
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> 79 Mir214 Mir214 134.69038 -3.216444 0.2154916 -14.926074 2.230149e-50 1.093947e-48 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
80 80
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> 81 Mir21 Mir21 26121.31011 2.963903 0.2008617 14.755939 2.817433e-49 1.312924e-47 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
82 82
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> 83 Mir1948 Mir1948 263.89527 7.074045 0.4867226 14.534039 7.374076e-48 3.272685e-46 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
84 84
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> 85 Mir27b Mir27b 76478.05753 -1.904653 0.1312889 -14.507339 1.088626e-47 4.611815e-46 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
86 86
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> 87 Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 14.184987 1.134862e-45 4.598659e-44 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
88 88
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> 89 Mir499 Mir499 712.45950 -10.577061 0.7528467 -14.049423 7.766426e-45 3.015962e-43 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
90 90
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> 91 Mir101b Mir101b 6846.19683 3.791681 0.2809666 13.495132 1.670548e-41 6.227801e-40 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
92 92
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> 93 Mir132 Mir132 106.46062 -2.797928 0.2083376 -13.429779 4.046171e-41 1.450397e-39 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
94 94
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> 95 Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 -12.868566 6.764677e-38 2.335066e-36 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
96 96
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> 97 Mir143 Mir143 179219.35960 -2.170303 0.1696199 -12.795094 1.746402e-37 5.813025e-36 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
98 98
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> 99 Mir155 Mir155 57.66182 -3.788079 0.3056585 -12.393175 2.845516e-35 9.144898e-34 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
100 100
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> 101 Mir322 Mir322 899.53469 -3.126011 0.2622596 -11.919531 9.363380e-33 2.908890e-31 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
102 102
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> 103 Mir378 Mir378 483.21548 -2.994300 0.2577321 -11.617876 3.343461e-31 1.005195e-29 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
104 104
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> 105 Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
106 106
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> 107 Mir3074-2 Mir3074-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
108 108
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> 109 Mir199b Mir199b 47.84725 -5.294373 0.4644474 -11.399295 4.215163e-30 1.155451e-28 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
110 110
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> 111 Mir802 Mir802 166.83414 8.816580 0.7782636 11.328527 9.478530e-30 2.523997e-28 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
112 112
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> 113 Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 -11.095122 1.324798e-28 3.429754e-27 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
114 114
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> 115 Mir301 Mir301 260.53406 -1.676984 0.1526772 -10.983852 4.570133e-28 1.151179e-26 2119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a>
116 116
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> 117 Snord104 Snord104 3851.90119 2.386573 0.2173857 10.978522 4.847915e-28 1.189015e-26 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
118 118
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> 119 Mir150 Mir150 553.20599 -2.836881 0.2595088 -10.931734 8.127991e-28 1.942381e-26 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
120 120
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> 121 Mir148a Mir148a 118994.46955 2.678852 0.2481801 10.793984 3.675045e-27 8.562855e-26 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
122 122
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> 123 5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 10.506053 8.101331e-26 1.841571e-24 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
124 124
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> 125 Mir193 Mir193 45.70861 4.991530 0.4814098 10.368568 3.446495e-25 7.647936e-24 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
126 126
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> 127 Mir3073 Mir3073 98.93199 8.208709 0.7944742 10.332254 5.036321e-25 1.091593e-23 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
128 128
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> 129 Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 -10.283590 8.355635e-25 1.769875e-23 609 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
130 130
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> 131 2610203C20Rik 2610203C20Rik 79.17666 -3.023491 0.2948614 -10.253939 1.136165e-24 2.353124e-23 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
132 132
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> 133 Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 -9.812740 9.923710e-23 2.010630e-21 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
134 134
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> 135 Mir184 Mir184 32.23796 -4.865023 0.4962776 -9.803028 1.092606e-22 2.166615e-21 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
136 136
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> 137 Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 -9.651880 4.826276e-22 9.371019e-21 352 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a>
138 138
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> 139 Mir182 Mir182 886.79583 4.919630 0.5101689 9.643140 5.255515e-22 9.996204e-21 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
140 140
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> 141 Snord91a Snord91a 168.95251 2.700421 0.2835464 9.523738 1.670595e-21 3.113990e-20 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
142 142
143 143
144 </pre> 144 </pre>
145 145
146 <div class="toolFormTitle">DifferentialCounts log output</div> 146 <div class="toolFormTitle">Differential images and outputs</div>
147 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
148 <div><table class="simple" cellpadding="2" cellspacing="2">
149 <tr>
150 <td><a href="Differential_rowsum_bar_charts.pdf"><img src="Differential_rowsum_bar_charts.png" title="Click to download a PDF of Differential_rowsum_bar_charts.pdf" hspace="5" width="400"
151 alt="Image called Differential_rowsum_bar_charts.pdf"/></a></td>
152
153 <td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf"><img src="Differential_venn_edgeRtest_significant_genes_overlap.png" title="Click to download a PDF of Differential_venn_edgeRtest_significant_genes_overlap.pdf" hspace="5" width="400"
154 alt="Image called Differential_venn_edgeRtest_significant_genes_overlap.pdf"/></a></td>
155 </tr>
156
157 </table></div>
158
159 <div class="toolFormTitle">Differential log output</div>
147 160
148 <pre> 161 <pre>
149 162
150 KernSmooth 2.23 loaded 163 [1] @@@ Quantiles for non-zero row counts:
151 164
152 Copyright M. P. Wand 1997-2009 165 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
166
167 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0
168
169 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
170
171 [1] "@@ using genecards substitution for urls"
172
173 [1] @@ Total low count contigs per sample = 1,1,1,1,1,1,1,1
174
175 [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
176
177 [1] Using design matrix:
178
179 (Intercept) groupliver
180
181 1 1 1
182
183 2 1 1
184
185 3 1 1
186
187 4 1 1
188
189 5 1 0
190
191 6 1 0
192
193 7 1 0
194
195 8 1 0
196
197 attr(,"assign")
198
199 [1] 0 1
200
201 attr(,"contrasts")
202
203 attr(,"contrasts")$group
204
205 [1] contr.treatment
206
207 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
208
209 [1] heart liver
210
211
212 </pre>
213
214 <div class="toolFormTitle">Differential log output</div>
215
216 <pre>
153 217
154 Attaching package: ‘gplots’ 218 Attaching package: ‘gplots’
155 219
156 The following object is masked from ‘package:stats’: 220 The following object is masked from ‘package:stats’:
157 221
158 lowess 222 lowess
159 223
224 Loading required package: methods
225
160 Loading required package: limma 226 Loading required package: limma
161 227
162 Loading required package: methods
163
164 Loading required package: splines 228 Loading required package: splines
165 229
166 Loading required package: DESeq2 230 Loading required package: DESeq2
167 231
168 Loading required package: GenomicRanges 232 Loading required package: GenomicRanges
185 249
186 xtabs 250 xtabs
187 251
188 The following objects are masked from ‘package:base’: 252 The following objects are masked from ‘package:base’:
189 253
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 254 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, 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
191 255
192 Loading required package: IRanges 256 Loading required package: IRanges
193 257
194 Attaching package: ‘IRanges’ 258 Attaching package: ‘IRanges’
195 259
196 The following object is masked from ‘package:gplots’: 260 The following object is masked from ‘package:gplots’:
197 261
198 space 262 space
199 263
200 Loading required package: GenomeInfoDb 264 Loading required package: XVector
201 265
202 Loading required package: Rcpp 266 Loading required package: Rcpp
203 267
204 Loading required package: RcppArmadillo 268 Loading required package: RcppArmadillo
205 269
207 271
208 mean-dispersion relationship 272 mean-dispersion relationship
209 273
210 final dispersion estimates 274 final dispersion estimates
211 275
212 Warning messages: 276 you had estimated gene-wise dispersions, removing these
213 277
214 1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : 278 you had estimated fitted dispersions, removing these
215 279
216 Outlier (-Inf) in boxplot 1 is not drawn 280 you had estimated gene-wise dispersions, removing these
217 281
218 2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : 282 you had estimated fitted dispersions, removing these
219 283
220 Outlier (-Inf) in boxplot 3 is not drawn 284 Warning message:
221 285
222 3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067, : 286 closing unused connection 4 (edgeR.log)
223 287
224 some notches went outside hinges ('box'): maybe set notch=FALSE 288 Warning message:
225 289
226 4: In par(defpar) : calling par(new=TRUE) with no plot 290 In sink() : no sink to remove
227 291
228 292
229 </pre> 293 </pre>
230 294
231 <div class="toolFormTitle">VOOM images and outputs</div> 295 <div class="toolFormTitle">VOOM images and outputs</div>
232 (Click on a thumbnail image to download the corresponding original PDF image)<br/> 296 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
233 <div><table class="simple" cellpadding="2" cellspacing="2"> 297 <div><table class="simple" cellpadding="2" cellspacing="2">
234 <tr> 298 <tr>
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" 299 <td><a href="VOOM_edgeRtest_mean_variance_plot.pdf"><img src="VOOM_edgeRtest_mean_variance_plot.png" title="Click to download a PDF of VOOM_edgeRtest_mean_variance_plot.pdf" hspace="5" width="400"
236 alt="Image called VOOM_DifferentialCounts_mean_variance_plot.pdf"/></a></td> 300 alt="Image called VOOM_edgeRtest_mean_variance_plot.pdf"/></a></td>
237 301
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" 302 <td><a href="VOOM_edgeRtest_qqplot.pdf"><img src="VOOM_edgeRtest_qqplot.png" title="Click to download a PDF of VOOM_edgeRtest_qqplot.pdf" hspace="5" width="400"
239 alt="Image called VOOM_DifferentialCounts_qqplot.pdf"/></a></td> 303 alt="Image called VOOM_edgeRtest_qqplot.pdf"/></a></td>
240 </tr> 304 </tr>
241 305
242 </table></div> 306 </table></div>
243 307
244 <div class="toolFormTitle">VOOM log output</div> 308 <div class="toolFormTitle">VOOM log output</div>
245 309
246 <pre> 310 <pre>
247 311
248 # VOOM top 50 312 # VOOM top 50
249 313
250 logFC AveExpr t P.Value adj.P.Val B NReads URL 314 Contig logFC AveExpr t P.Value adj.P.Val B NReads URL
251 315
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> 316 Mir192 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>
253 317
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> 318 Mir208a 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>
255 319
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> 320 Mir3073 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>
257 321
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> 322 Mir802 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>
259 323
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> 324 Mir208b 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>
261 325
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> 326 Mir499 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>
263 327
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> 328 Mir10b 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>
265 329
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> 330 Mir148a 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>
267 331
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> 332 Mir490 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>
269 333
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> 334 Mir122a 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>
271 335
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> 336 Mir133b 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>
273 337
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> 338 Mir149 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>
275 339
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> 340 Mir101b 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>
277 341
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> 342 Mir143 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>
279 343
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> 344 Mir194-2 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>
281 345
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> 346 Mir23a 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>
283 347
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> 348 Mir1983 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>
285 349
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> 350 Mir27a 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>
287 351
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> 352 Cyp3a25 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>
289 353
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> 354 Mir200a 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>
291 355
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> 356 Mir181d 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>
293 357
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> 358 Mir153 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>
295 359
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> 360 Mir204 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>
297 361
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> 362 Gm5441 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>
299 363
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> 364 Rabggtb 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>
301 365
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> 366 Mir504 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>
303 367
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> 368 Mir133a-1 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>
305 369
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> 370 Mir195 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>
307 371
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> 372 Mir27b 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>
309 373
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> 374 Snord52 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>
311 375
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> 376 Mir322 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>
313 377
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> 378 Mir181c 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>
315 379
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> 380 Mir1948 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>
317 381
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> 382 0610031O16Rik 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>
319 383
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> 384 Mir201 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>
321 385
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> 386 Mir21 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>
323 387
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> 388 Mir184 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>
325 389
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> 390 1810019D21Rik 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>
327 391
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> 392 Mir203 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>
329 393
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> 394 1110038B12Rik 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>
331 395
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> 396 Snord104 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>
333 397
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> 398 Mir182 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>
335 399
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> 400 Mir547 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>
337 401
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> 402 Mir143hg 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>
339 403
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> 404 Scnn1b 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>
341 405
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> 406 Mir125b-2 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>
343 407
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> 408 Mir1a-1 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>
345 409
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> 410 Mir378 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>
347 411
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> 412 Mir199b 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>
349 413
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> 414 Mir155 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>
351 415
352 416
353 </pre> 417 </pre>
354 418
355 <div class="toolFormTitle">edgeR images and outputs</div> 419 <div class="toolFormTitle">edgeR images and outputs</div>
356 (Click on a thumbnail image to download the corresponding original PDF image)<br/> 420 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
357 <div><table class="simple" cellpadding="2" cellspacing="2"> 421 <div><table class="simple" cellpadding="2" cellspacing="2">
358 <tr> 422 <tr>
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" 423 <td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf"><img src="edgeR_edgeRtest_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400"
360 alt="Image called edgeR_DifferentialCounts_BCV_vs_abundance.pdf"/></a></td> 424 alt="Image called edgeR_edgeRtest_BCV_vs_abundance.pdf"/></a></td>
361 425
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" 426 <td><a href="edgeR_edgeRtest_GoodnessofFit.pdf"><img src="edgeR_edgeRtest_GoodnessofFit.png" title="Click to download a PDF of edgeR_edgeRtest_GoodnessofFit.pdf" hspace="5" width="400"
363 alt="Image called edgeR_DifferentialCounts_GoodnessofFit.pdf"/></a></td> 427 alt="Image called edgeR_edgeRtest_GoodnessofFit.pdf"/></a></td>
364 428
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" 429 <td><a href="edgeR_edgeRtest_MDSplot.pdf"><img src="edgeR_edgeRtest_MDSplot.png" title="Click to download a PDF of edgeR_edgeRtest_MDSplot.pdf" hspace="5" width="400"
366 alt="Image called edgeR_DifferentialCounts_MDSplot.pdf"/></a></td> 430 alt="Image called edgeR_edgeRtest_MDSplot.pdf"/></a></td>
367 </tr> 431 </tr>
368 <tr> 432 <tr>
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" 433 <td><a href="edgeR_edgeRtest_qqplot.pdf"><img src="edgeR_edgeRtest_qqplot.png" title="Click to download a PDF of edgeR_edgeRtest_qqplot.pdf" hspace="5" width="400"
370 alt="Image called edgeR_DifferentialCounts_qqplot.pdf"/></a></td> 434 alt="Image called edgeR_edgeRtest_qqplot.pdf"/></a></td>
371 435
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" 436 <td><a href="edgeR_edgeRtest_smearplot.pdf"><img src="edgeR_edgeRtest_smearplot.png" title="Click to download a PDF of edgeR_edgeRtest_smearplot.pdf" hspace="5" width="400"
373 alt="Image called edgeR_DifferentialCounts_raw_norm_counts_box.pdf"/></a></td> 437 alt="Image called edgeR_edgeRtest_smearplot.pdf"/></a></td>
374 438
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" 439 <td><a href="edgeR_edgeRtest_top_100_heatmap.pdf"><img src="edgeR_edgeRtest_top_100_heatmap.png" title="Click to download a PDF of edgeR_edgeRtest_top_100_heatmap.pdf" hspace="5" width="400"
376 alt="Image called edgeR_DifferentialCounts_smearplot.pdf"/></a></td> 440 alt="Image called edgeR_edgeRtest_top_100_heatmap.pdf"/></a></td>
377 </tr> 441 </tr>
378 <tr> 442
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" 443 </table></div>
380 alt="Image called edgeR_DifferentialCounts_top_100_heatmap.pdf"/></a></td>
381
382 <td>&nbsp;</td><td>&nbsp;</td>
383 </tr></table></div>
384 444
385 <div class="toolFormTitle">edgeR log output</div> 445 <div class="toolFormTitle">edgeR log output</div>
386 446
387 <pre> 447 <pre>
388 448
389 [1] Common Dispersion = 0.228651459675839 CV = 0.478175134940995 getPriorN = 3.33333333333333 449 [1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333
390 450
391 [1] "No GLM fit outlier genes found\n" 451 [1] "No GLM fit outlier genes found\n"
392 452
393 [1] Heart Liver 453 [1] @@ edgeR Top tags\n
394
395 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
396
397 [1] raw contig counts by sample:
398
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
400
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
402
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
404
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
406
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
408
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
410
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
412
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
414
415 [1] normalised contig counts by sample:
416
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
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
434 454
435 Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL 455 Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL
436 456
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> 457 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>
438 458
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> 459 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>
440 460
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> 461 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>
442 462
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> 463 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>
444 464
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> 465 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>
446 466
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> 467 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>
448 468
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> 469 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>
450 470
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> 471 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>
452 472
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> 473 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>
454 474
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> 475 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>
456 476
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> 477 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>
458 478
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> 479 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>
460 480
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> 481 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>
462 482
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> 483 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>
464 484
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> 485 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>
466 486
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> 487 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>
468 488
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> 489 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>
470 490
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> 491 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>
472 492
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> 493 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>
474 494
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> 495 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>
476 496
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> 497 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>
478 498
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> 499 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>
480 500
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> 501 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>
482 502
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> 503 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>
484 504
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> 505 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>
486 506
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> 507 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>
488 508
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> 509 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>
490 510
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> 511 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>
492 512
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> 513 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>
494 514
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> 515 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>
496 516
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> 517 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>
498 518
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> 519 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>
500 520
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> 521 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>
502 522
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> 523 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>
504 524
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> 525 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>
506 526
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> 527 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>
508 528
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> 529 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>
510 530
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> 531 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>
512 532
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> 533 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>
514 534
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> 535 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>
516 536
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> 537 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>
518 538
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> 539 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>
520 540
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> 541 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>
522 542
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> 543 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>
524 544
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> 545 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>
526 546
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> 547 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>
528 548
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> 549 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>
530 550
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> 551 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>
532 552
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> 553 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>
534 554
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> 555 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>
536 556
537 [1] # 416 tags significant at adj p= 0.05 557 [1] @@ 416 tags significant at adj p= 0.05
538 558
539 559
540 </pre> 560 </pre>
541 561
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
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>
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"
554 alt="Image called sample_counts_histogram.pdf"/></a></td>
555
556 <td>&nbsp;</td>
557 </tr></table></div>
558
559 <div class="toolFormTitle">Other log output</div> 562 <div class="toolFormTitle">Other log output</div>
560 563
561 <pre> 564 <pre>
562 565
563 ## Toolfactory generated command line = Rscript - None None 566 ## Toolfactory generated command line = Rscript - None None
564 567
565 Got TCols=1 5 6 7; CCols=2 3 4 8 568 Got TCols=1 5 6 7; CCols=2 3 4 8
566 569
567 [1] # Quantiles for non-zero row counts: 570 R version 3.0.2 (2013-09-25)
568 571
569 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 572 Platform: x86_64-pc-linux-gnu (64-bit)
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
577 [1] # urls sample
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
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
584
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
586
587 [1] Using design matrix:
588
589 (Intercept) groupLiver
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
617 R version 3.1.0 (2014-04-10)
618
619 Platform: x86_64-unknown-linux-gnu (64-bit)
620 573
621 locale: 574 locale:
622 575
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 576 [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
624 577
626 579
627 [1] parallel splines methods stats graphics grDevices utils datasets base 580 [1] parallel splines methods stats graphics grDevices utils datasets base
628 581
629 other attached packages: 582 other attached packages:
630 583
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_0.6.2 584 [1] RColorBrewer_1.0-5 DESeq2_1.2.10 RcppArmadillo_0.4.400.0 Rcpp_0.11.2 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 BiocGenerics_0.8.0 edgeR_3.4.2 limma_3.18.13 gplots_2.15.0 stringr_0.6.2
632 585
633 loaded via a namespace (and not attached): 586 loaded via a namespace (and not attached):
634 587
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_0.4.0 588 [1] annotate_1.40.1 AnnotationDbi_1.24.0 Biobase_2.22.0 bitops_1.0-6 caTools_1.17.1 DBI_0.3.0 gdata_2.13.3 genefilter_1.44.0 grid_3.0.2 gtools_3.4.1 KernSmooth_2.23-13 lattice_0.20-29 locfit_1.5-9.1 RSQLite_0.11.4 stats4_3.0.2 survival_2.37-7 XML_3.98-1.1 xtable_1.7-4
636 589
637 590
638 </pre> 591 </pre>
639 592
640 <div class="toolFormTitle">All output files available for downloading</div> 593 <div class="toolFormTitle">All output files available for downloading</div>
641 594
642 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> 595 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
643 596
644 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr> 597 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr>
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> 598 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_MA_plot.pdf">DESeq2_edgeRtest_MA_plot.pdf</a></td><td>15.0 KB</td></tr>
646 <tr><td><a href="DESeq2_DifferentialCounts_PCA_plot.pdf">DESeq2_DifferentialCounts_PCA_plot.pdf</a></td><td>4.9 KB</td></tr> 599 <tr><td><a href="DESeq2_edgeRtest_PCA_plot.pdf">DESeq2_edgeRtest_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
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> 600 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf">DESeq2_edgeRtest_dispersion_estimates.pdf</a></td><td>190.6 KB</td></tr>
648 <tr><td><a href="DESeq2_DifferentialCounts_qqplot.pdf">DESeq2_DifferentialCounts_qqplot.pdf</a></td><td>12.8 KB</td></tr> 601 <tr><td><a href="DESeq2_edgeRtest_qqplot.pdf">DESeq2_edgeRtest_qqplot.pdf</a></td><td>13.3 KB</td></tr>
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> 602 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf">DESeq2_edgeRtest_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>
650 <tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>28.4 KB</td></tr> 603 <tr><td><a href="Differential.log">Differential.log</a></td><td>1.4 KB</td></tr>
651 <tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>2.0 KB</td></tr> 604 <tr class="odd_row"><td><a href="Differential_Counts.Rscript">Differential_Counts.Rscript</a></td><td>28.3 KB</td></tr>
652 <tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.5 KB</td></tr> 605 <tr><td><a href="Differential_Counts_error.log">Differential_Counts_error.log</a></td><td>1.8 KB</td></tr>
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> 606 <tr class="odd_row"><td><a href="Differential_Counts_runner.log">Differential_Counts_runner.log</a></td><td>1.3 KB</td></tr>
654 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>9.4 KB</td></tr> 607 <tr><td><a href="Differential_rowsum_bar_charts.pdf">Differential_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>
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> 608 <tr class="odd_row"><td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf">Differential_venn_edgeRtest_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>
656 <tr><td><a href="VOOM_DifferentialCounts_qqplot.pdf">VOOM_DifferentialCounts_qqplot.pdf</a></td><td>17.5 KB</td></tr> 609 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>
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> 610 <tr class="odd_row"><td><a href="VOOM_edgeRtest_mean_variance_plot.pdf">VOOM_edgeRtest_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>
658 <tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr> 611 <tr><td><a href="VOOM_edgeRtest_qqplot.pdf">VOOM_edgeRtest_qqplot.pdf</a></td><td>17.5 KB</td></tr>
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> 612 <tr class="odd_row"><td><a href="edgeR.log">edgeR.log</a></td><td>10.4 KB</td></tr>
660 <tr><td><a href="edgeR_DifferentialCounts_GoodnessofFit.pdf">edgeR_DifferentialCounts_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr> 613 <tr><td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf">edgeR_edgeRtest_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
661 <tr class="odd_row"><td><a href="edgeR_DifferentialCounts_MDSplot.pdf">edgeR_DifferentialCounts_MDSplot.pdf</a></td><td>5.0 KB</td></tr> 614 <tr class="odd_row"><td><a href="edgeR_edgeRtest_GoodnessofFit.pdf">edgeR_edgeRtest_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
662 <tr><td><a href="edgeR_DifferentialCounts_qqplot.pdf">edgeR_DifferentialCounts_qqplot.pdf</a></td><td>15.2 KB</td></tr> 615 <tr><td><a href="edgeR_edgeRtest_MDSplot.pdf">edgeR_edgeRtest_MDSplot.pdf</a></td><td>4.9 KB</td></tr>
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> 616 <tr class="odd_row"><td><a href="edgeR_edgeRtest_qqplot.pdf">edgeR_edgeRtest_qqplot.pdf</a></td><td>15.2 KB</td></tr>
664 <tr><td><a href="edgeR_DifferentialCounts_smearplot.pdf">edgeR_DifferentialCounts_smearplot.pdf</a></td><td>16.6 KB</td></tr> 617 <tr><td><a href="edgeR_edgeRtest_smearplot.pdf">edgeR_edgeRtest_smearplot.pdf</a></td><td>16.7 KB</td></tr>
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> 618 <tr class="odd_row"><td><a href="edgeR_edgeRtest_top_100_heatmap.pdf">edgeR_edgeRtest_top_100_heatmap.pdf</a></td><td>11.2 KB</td></tr>
666 <tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr>
667 </table></div><br/> 619 </table></div><br/>
668 </div></body></html> 620 </div></body></html>
669 621