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comparison test-data/edgeRtest1out.html @ 111:9f2e0ec3e826 draft

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author fubar
date Wed, 22 Oct 2014 23:37:31 -0400
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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"> 1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> 4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://getgalaxy.org/" />
5 <title></title> 5 <title></title>
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 07/08/2013 15:46:55</div><br/> 11 <div class="infomessage">Galaxy Tool "DifferentialCounts" run at 06/10/2014 15:33:02</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_MA_plot.pdf"><img src="DESeq2_MA_plot.png" title="Click to download a PDF of DESeq2_MA_plot.pdf" hspace="5" width="400" 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"
17 alt="Image called DESeq2_MA_plot.pdf"/></a></td> 17 alt="Image called DESeq2_DifferentialCounts_MA_plot.pdf"/></a></td>
18 18
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" 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"
20 alt="Image called DESeq2_PCA_plot.pdf"/></a></td> 20 alt="Image called DESeq2_DifferentialCounts_PCA_plot.pdf"/></a></td>
21 21
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" 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"
23 alt="Image called DESeq2_dispersion_estimates.pdf"/></a></td> 23 alt="Image called DESeq2_DifferentialCounts_dispersion_estimates.pdf"/></a></td>
24 </tr> 24 </tr>
25 <tr> 25 <tr>
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" 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"
27 alt="Image called DESeq2_qqplot.pdf"/></a></td> 27 alt="Image called DESeq2_DifferentialCounts_qqplot.pdf"/></a></td>
28 28
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" 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"
30 alt="Image called DESeq2_sample_distance_plot.pdf"/></a></td> 30 alt="Image called DESeq2_DifferentialCounts_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>
36 36
37 <pre> 37 <pre>
38 38
39 # DESeq top 50 39 # DESeq top 50
40 40
41 Contig baseMean log2FoldChange lfcSE pvalue padj NReads URL 41 Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL
42 42
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> 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>
44 44
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> 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>
46 46
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> 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>
48 48
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> 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>
50 50
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> 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>
52 52
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> 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>
54 54
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> 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>
56 56
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> 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>
58 58
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> 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>
60 60
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> 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>
62 62
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> 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>
64 64
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> 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>
66 66
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> 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>
68 68
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> 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>
70 70
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> 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>
72 72
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> 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>
74 74
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> 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>
76 76
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> 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>
78 78
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> 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>
80 80
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> 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>
82 82
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> 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>
84 84
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> 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>
86 86
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> 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>
88 88
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> 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>
90 90
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> 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>
92 92
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> 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>
94 94
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> 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>
96 96
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> 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>
98 98
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> 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>
100 100
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> 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>
102 102
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> 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>
104 104
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> 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>
106 106
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> 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>
108 108
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> 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>
110 110
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> 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>
112 112
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> 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>
114 114
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> 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>
116 116
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> 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>
118 118
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> 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>
120 120
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> 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>
122 122
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> 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>
124 124
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> 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>
126 126
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> 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>
128 128
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> 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>
130 130
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> 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>
132 132
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> 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>
134 134
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> 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>
136 136
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> 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>
138 138
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> 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>
140 140
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> 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>
142 142
143 143
144 </pre> 144 </pre>
145 145
146 <div class="toolFormTitle">DifferentialCounts log output</div> 146 <div class="toolFormTitle">DifferentialCounts log output</div>
147 147
148 <pre> 148 <pre>
149 149
150 Loading required package: gtools 150 KernSmooth 2.23 loaded
151 151
152 Loading required package: gdata 152 Copyright M. P. Wand 1997-2009
153 153
154 gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. 154 Attaching package: ‘gplots’
155
156 gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
157
158 Attaching package: ‘gdata’
159 155
160 The following object is masked from ‘package:stats’: 156 The following object is masked from ‘package:stats’:
161 157
162 nobs 158 lowess
163 159
164 The following object is masked from ‘package:utils’: 160 Loading required package: limma
165 161
166 object.size 162 Loading required package: methods
167 163
168 Loading required package: caTools 164 Loading required package: splines
169 165
170 Loading required package: grid 166 Loading required package: DESeq2
171 167
172 Loading required package: KernSmooth 168 Loading required package: GenomicRanges
173 169
174 KernSmooth 2.23 loaded 170 Loading required package: BiocGenerics
175 171
176 Copyright M. P. Wand 1997-2009 172 Loading required package: parallel
177 173
178 Loading required package: MASS 174 Attaching package: ‘BiocGenerics’
179 175
180 Attaching package: ‘gplots’ 176 The following objects are masked from ‘package:parallel’:
177
178 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
179
180 The following object is masked from ‘package:limma’:
181
182 plotMA
181 183
182 The following object is masked from ‘package:stats’: 184 The following object is masked from ‘package:stats’:
183 185
184 lowess
185
186 Loading required package: methods
187
188 Loading required package: limma
189
190 Loading required package: splines
191
192 Loading required package: DESeq2
193
194 Loading required package: GenomicRanges
195
196 Loading required package: BiocGenerics
197
198 Loading required package: parallel
199
200 Attaching package: ‘BiocGenerics’
201
202 The following object is masked from ‘package:parallel’:
203
204 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
205
206 The following object is masked from ‘package:gdata’:
207
208 combine
209
210 The following object is masked from ‘package:stats’:
211
212 xtabs 186 xtabs
213 187
214 The following object is masked from ‘package:base’: 188 The following objects are masked from ‘package:base’:
215 189
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 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
217 191
218 Loading required package: IRanges 192 Loading required package: IRanges
219 193
220 Attaching package: ‘IRanges’ 194 Attaching package: ‘IRanges’
221 195
222 The following object is masked from ‘package:gplots’: 196 The following object is masked from ‘package:gplots’:
223 197
224 space 198 space
225 199
226 The following object is masked from ‘package:caTools’: 200 Loading required package: GenomeInfoDb
227
228 runmean
229
230 The following object is masked from ‘package:gdata’:
231
232 trim
233
234 Loading required package: Biobase
235
236 Welcome to Bioconductor
237
238 Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
239
240 Loading required package: lattice
241 201
242 Loading required package: Rcpp 202 Loading required package: Rcpp
243 203
244 Loading required package: RcppArmadillo 204 Loading required package: RcppArmadillo
245
246 Attaching package: ‘DESeq2’
247
248 The following object is masked from ‘package:limma’:
249
250 plotMA
251
252 gene-wise dispersion estimates
253
254 mean-dispersion relationship
255
256 final dispersion estimates
257
258 you had estimated dispersions, replacing these
259
260 gene-wise dispersion estimates
261
262 mean-dispersion relationship
263
264 final dispersion estimates
265
266 you had estimated dispersions, replacing these
267 205
268 gene-wise dispersion estimates 206 gene-wise dispersion estimates
269 207
270 mean-dispersion relationship 208 mean-dispersion relationship
271 209
292 230
293 <div class="toolFormTitle">VOOM images and outputs</div> 231 <div class="toolFormTitle">VOOM images and outputs</div>
294 (Click on a thumbnail image to download the corresponding original PDF image)<br/> 232 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
295 <div><table class="simple" cellpadding="2" cellspacing="2"> 233 <div><table class="simple" cellpadding="2" cellspacing="2">
296 <tr> 234 <tr>
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" 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"
298 alt="Image called VOOM_mean_variance_plot.pdf"/></a></td> 236 alt="Image called VOOM_DifferentialCounts_mean_variance_plot.pdf"/></a></td>
299 237
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" 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"
301 alt="Image called VOOM_qqplot.pdf"/></a></td> 239 alt="Image called VOOM_DifferentialCounts_qqplot.pdf"/></a></td>
302 </tr> 240 </tr>
303 241
304 </table></div> 242 </table></div>
305 243
306 <div class="toolFormTitle">VOOM log output</div> 244 <div class="toolFormTitle">VOOM log output</div>
307 245
308 <pre> 246 <pre>
309 247
310 # VOOM top 50 248 # VOOM top 50
311 249
312 ID logFC AveExpr t P.Value adj.P.Val B NReads URL 250 logFC AveExpr t P.Value adj.P.Val B NReads URL
313 251
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> 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>
315 253
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> 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>
317 255
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> 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>
319 257
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> 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>
321 259
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> 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>
323 261
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> 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>
325 263
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> 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>
327 265
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> 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>
329 267
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> 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>
331 269
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> 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>
333 271
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> 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>
335 273
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> 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>
337 275
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> 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>
339 277
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> 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>
341 279
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> 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>
343 281
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> 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>
345 283
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> 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>
347 285
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> 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>
349 287
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> 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>
351 289
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> 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>
353 291
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> 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>
355 293
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> 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>
357 295
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> 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>
359 297
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> 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>
361 299
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> 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>
363 301
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> 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>
365 303
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> 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>
367 305
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> 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>
369 307
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> 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>
371 309
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> 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>
373 311
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> 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>
375 313
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> 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>
377 315
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> 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>
379 317
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> 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>
381 319
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> 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>
383 321
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> 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>
385 323
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> 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>
387 325
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> 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>
389 327
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> 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>
391 329
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> 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>
393 331
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> 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>
395 333
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> 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>
397 335
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> 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>
399 337
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> 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>
401 339
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> 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>
403 341
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> 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>
405 343
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> 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>
407 345
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> 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>
409 347
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> 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>
411 349
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> 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>
413 351
414 352
415 </pre> 353 </pre>
416 354
417 <div class="toolFormTitle">edgeR images and outputs</div> 355 <div class="toolFormTitle">edgeR images and outputs</div>
418 (Click on a thumbnail image to download the corresponding original PDF image)<br/> 356 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
419 <div><table class="simple" cellpadding="2" cellspacing="2"> 357 <div><table class="simple" cellpadding="2" cellspacing="2">
420 <tr> 358 <tr>
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" 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"
422 alt="Image called edgeR_BCV_vs_abundance.pdf"/></a></td> 360 alt="Image called edgeR_DifferentialCounts_BCV_vs_abundance.pdf"/></a></td>
423 361
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" 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"
425 alt="Image called edgeR_GoodnessofFit.pdf"/></a></td> 363 alt="Image called edgeR_DifferentialCounts_GoodnessofFit.pdf"/></a></td>
426 364
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" 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"
428 alt="Image called edgeR_MDSplot.pdf"/></a></td> 366 alt="Image called edgeR_DifferentialCounts_MDSplot.pdf"/></a></td>
429 </tr> 367 </tr>
430 <tr> 368 <tr>
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" 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"
432 alt="Image called edgeR_qqplot.pdf"/></a></td> 370 alt="Image called edgeR_DifferentialCounts_qqplot.pdf"/></a></td>
433 371
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" 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"
435 alt="Image called edgeR_raw_norm_counts_box.pdf"/></a></td> 373 alt="Image called edgeR_DifferentialCounts_raw_norm_counts_box.pdf"/></a></td>
436 374
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" 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"
438 alt="Image called edgeR_smearplot.pdf"/></a></td> 376 alt="Image called edgeR_DifferentialCounts_smearplot.pdf"/></a></td>
439 </tr> 377 </tr>
440 <tr> 378 <tr>
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" 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"
442 alt="Image called edgeR_top_100_heatmap.pdf"/></a></td> 380 alt="Image called edgeR_DifferentialCounts_top_100_heatmap.pdf"/></a></td>
443 381
444 <td>&nbsp;</td><td>&nbsp;</td> 382 <td>&nbsp;</td><td>&nbsp;</td>
445 </tr></table></div> 383 </tr></table></div>
446 384
447 <div class="toolFormTitle">edgeR log output</div> 385 <div class="toolFormTitle">edgeR log output</div>
448 386
449 <pre> 387 <pre>
450 388
451 [1] prior.df = 8 389 [1] Common Dispersion = 0.228651459675839 CV = 0.478175134940995 getPriorN = 3.33333333333333
452 390
453 [1] "No GLM fit outlier genes found\n" 391 [1] "No GLM fit outlier genes found\n"
454 392
455 [1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333 393 [1] Heart Liver
456
457 [1] heart liver
458 394
459 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365" 395 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
460 396
461 [1] raw contig counts by sample: 397 [1] raw contig counts by sample:
462 398
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 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
464 400
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 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
466 402
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 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
468 404
476 412
477 NA's :650 NA's :969 NA's :664 NA's :886 NA's :902 NA's :957 NA's :821 NA's :950 413 NA's :650 NA's :969 NA's :664 NA's :886 NA's :902 NA's :957 NA's :821 NA's :950
478 414
479 [1] normalised contig counts by sample: 415 [1] normalised contig counts by sample:
480 416
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 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
482 418
483 Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf 419 Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf
484 420
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 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
486 422
500 436
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> 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>
502 438
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> 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>
504 440
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> 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>
506 442
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> 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>
508 444
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> 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>
510 446
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> 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>
512 448
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> 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>
514 450
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> 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>
516 452
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> 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>
518 454
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> 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>
520 456
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> 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>
522 458
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> 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>
524 460
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> 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>
526 462
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> 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>
528 464
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> 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>
530 466
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> 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>
532 468
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> 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>
534 470
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> 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>
536 472
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> 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>
538 474
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> 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>
540 476
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> 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>
542 478
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> 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>
544 480
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> 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>
546 482
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> 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>
548 484
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> 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>
550 486
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> 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>
552 488
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> 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>
554 490
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> 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>
556 492
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> 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>
558 494
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> 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>
560 496
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> 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>
562 498
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> 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>
564 500
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> 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>
566 502
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> 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>
568 504
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> 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>
570 506
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> 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>
572 508
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> 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>
574 510
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> 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>
576 512
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> 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>
578 514
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> 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>
580 516
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> 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>
582 518
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> 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>
584 520
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> 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>
586 522
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> 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>
588 524
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> 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>
590 526
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> 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>
592 528
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> 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>
594 530
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> 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>
596 532
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> 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>
598 534
608 <div><table class="simple" cellpadding="2" cellspacing="2"> 544 <div><table class="simple" cellpadding="2" cellspacing="2">
609 <tr> 545 <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" 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"
611 alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td> 547 alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td>
612 548
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" 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"
614 alt="Image called Venn_significant_genes_overlap.pdf"/></a></td> 550 alt="Image called Venn_DifferentialCounts_significant_genes_overlap.pdf"/></a></td>
615 </tr> 551 </tr>
616 <tr> 552 <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" 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"
618 alt="Image called sample_counts_histogram.pdf"/></a></td> 554 alt="Image called sample_counts_histogram.pdf"/></a></td>
619 555
636 572
637 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs 573 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
638 574
639 [1] "@@ using genecards substitution for urls" 575 [1] "@@ using genecards substitution for urls"
640 576
641 [1] # urls 577 [1] # urls sample
642 578
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> 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>
644 580
645 [6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a> 581 [6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
646 582
647 [1] # Total low count contigs per sample = 170,67,203,86,145,111,155,120 583 [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
648 584
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 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
650 586
651 [1] Using design matrix: 587 [1] Using design matrix:
652 588
653 (Intercept) groupliver 589 (Intercept) groupLiver
654 590
655 1 1 1 591 1 1 1
656 592
657 2 1 1 593 2 1 1
658 594
676 612
677 attr(,"contrasts")$group 613 attr(,"contrasts")$group
678 614
679 [1] contr.treatment 615 [1] contr.treatment
680 616
681 R version 3.0.1 (2013-05-16) 617 R version 3.1.0 (2014-04-10)
682 618
683 Platform: x86_64-unknown-linux-gnu (64-bit) 619 Platform: x86_64-unknown-linux-gnu (64-bit)
684 620
685 locale: 621 locale:
686 622
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 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
688 624
689 attached base packages: 625 attached base packages:
690 626
691 [1] parallel splines methods grid stats graphics grDevices utils datasets base 627 [1] parallel splines methods stats graphics grDevices utils datasets base
692 628
693 other attached packages: 629 other attached packages:
694 630
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_0.6.2 631 [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
696 632
697 loaded via a namespace (and not attached): 633 loaded via a namespace (and not attached):
698 634
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_1.7-1 635 [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
700 636
701 637
702 </pre> 638 </pre>
703 639
704 <div class="toolFormTitle">All output files available for downloading</div> 640 <div class="toolFormTitle">All output files available for downloading</div>
705 641
706 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> 642 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
707 643
708 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.0 KB</td></tr> 644 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr>
709 <tr class="odd_row"><td><a href="DESeq2_MA_plot.pdf">DESeq2_MA_plot.pdf</a></td><td>14.7 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>
710 <tr><td><a href="DESeq2_PCA_plot.pdf">DESeq2_PCA_plot.pdf</a></td><td>4.9 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>
711 <tr class="odd_row"><td><a href="DESeq2_dispersion_estimates.pdf">DESeq2_dispersion_estimates.pdf</a></td><td>188.4 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>
712 <tr><td><a href="DESeq2_qqplot.pdf">DESeq2_qqplot.pdf</a></td><td>14.4 KB</td></tr> 648 <tr><td><a href="DESeq2_DifferentialCounts_qqplot.pdf">DESeq2_DifferentialCounts_qqplot.pdf</a></td><td>12.8 KB</td></tr>
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> 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>
714 <tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>27.1 KB</td></tr> 650 <tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>28.4 KB</td></tr>
715 <tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>3.1 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>
716 <tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.2 KB</td></tr> 652 <tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.5 KB</td></tr>
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> 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>
718 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr> 654 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>9.4 KB</td></tr>
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> 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>
720 <tr><td><a href="VOOM_qqplot.pdf">VOOM_qqplot.pdf</a></td><td>17.6 KB</td></tr> 656 <tr><td><a href="VOOM_DifferentialCounts_qqplot.pdf">VOOM_DifferentialCounts_qqplot.pdf</a></td><td>17.5 KB</td></tr>
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> 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>
722 <tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr> 658 <tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr>
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> 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>
724 <tr><td><a href="edgeR_GoodnessofFit.pdf">edgeR_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr> 660 <tr><td><a href="edgeR_DifferentialCounts_GoodnessofFit.pdf">edgeR_DifferentialCounts_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
725 <tr class="odd_row"><td><a href="edgeR_MDSplot.pdf">edgeR_MDSplot.pdf</a></td><td>4.9 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>
726 <tr><td><a href="edgeR_qqplot.pdf">edgeR_qqplot.pdf</a></td><td>15.2 KB</td></tr> 662 <tr><td><a href="edgeR_DifferentialCounts_qqplot.pdf">edgeR_DifferentialCounts_qqplot.pdf</a></td><td>15.2 KB</td></tr>
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> 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>
728 <tr><td><a href="edgeR_smearplot.pdf">edgeR_smearplot.pdf</a></td><td>16.6 KB</td></tr> 664 <tr><td><a href="edgeR_DifferentialCounts_smearplot.pdf">edgeR_DifferentialCounts_smearplot.pdf</a></td><td>16.6 KB</td></tr>
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> 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>
730 <tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr> 666 <tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr>
731 </table></div><br/> 667 </table></div><br/>
732 </div></body></html> 668 </div></body></html>
733 669