Mercurial > repos > fubar > differential_count_models
diff test-data/edgeRtest1out.html @ 111:9f2e0ec3e826 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 22 Oct 2014 23:37:31 -0400 |
| parents | c0fa3dde02d9 |
| children | a9ffdf5f7d2a |
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--- a/test-data/edgeRtest1out.html Sun Jul 06 21:00:54 2014 -0400 +++ b/test-data/edgeRtest1out.html Wed Oct 22 23:37:31 2014 -0400 @@ -1,33 +1,33 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> + <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://getgalaxy.org/" /> <title></title> <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> </head> <body> <div class="toolFormBody"> -<div class="infomessage">Galaxy Tool "DifferentialCounts" run at 07/08/2013 15:46:55</div><br/> +<div class="infomessage">Galaxy Tool "DifferentialCounts" run at 06/10/2014 15:33:02</div><br/> <div class="toolFormTitle">DESeq2 images and outputs</div> (Click on a thumbnail image to download the corresponding original PDF image)<br/> <div><table class="simple" cellpadding="2" cellspacing="2"> <tr> -<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" - alt="Image called DESeq2_MA_plot.pdf"/></a></td> +<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" + alt="Image called DESeq2_DifferentialCounts_MA_plot.pdf"/></a></td> -<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" - alt="Image called DESeq2_PCA_plot.pdf"/></a></td> +<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" + alt="Image called DESeq2_DifferentialCounts_PCA_plot.pdf"/></a></td> -<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" - alt="Image called DESeq2_dispersion_estimates.pdf"/></a></td> +<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" + alt="Image called DESeq2_DifferentialCounts_dispersion_estimates.pdf"/></a></td> </tr> <tr> -<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" - alt="Image called DESeq2_qqplot.pdf"/></a></td> +<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" + alt="Image called DESeq2_DifferentialCounts_qqplot.pdf"/></a></td> -<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" - alt="Image called DESeq2_sample_distance_plot.pdf"/></a></td> +<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" + alt="Image called DESeq2_DifferentialCounts_sample_distance_plot.pdf"/></a></td> <td> </td> </tr></table></div> @@ -38,107 +38,107 @@ # DESeq top 50 - Contig baseMean log2FoldChange lfcSE pvalue padj NReads URL + Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> </pre> @@ -147,45 +147,19 @@ <pre> -Loading required package: gtools - -Loading required package: gdata - -gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. - -gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. - -Attaching package: ‘gdata’ - -The following object is masked from ‘package:stats’: - - nobs - -The following object is masked from ‘package:utils’: - - object.size - -Loading required package: caTools - -Loading required package: grid - -Loading required package: KernSmooth - KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 -Loading required package: MASS - Attaching package: ‘gplots’ The following object is masked from ‘package:stats’: lowess -Loading required package: methods +Loading required package: limma -Loading required package: limma +Loading required package: methods Loading required package: splines @@ -199,21 +173,21 @@ Attaching package: ‘BiocGenerics’ -The following object is masked from ‘package:parallel’: +The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB -The following object is masked from ‘package:gdata’: +The following object is masked from ‘package:limma’: - combine + plotMA The following object is masked from ‘package:stats’: xtabs -The following object is masked from ‘package:base’: +The following objects are masked from ‘package:base’: - 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 + 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 Loading required package: IRanges @@ -223,48 +197,12 @@ space -The following object is masked from ‘package:caTools’: - - runmean - -The following object is masked from ‘package:gdata’: - - trim - -Loading required package: Biobase - -Welcome to Bioconductor - - Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. - -Loading required package: lattice +Loading required package: GenomeInfoDb Loading required package: Rcpp Loading required package: RcppArmadillo -Attaching package: ‘DESeq2’ - -The following object is masked from ‘package:limma’: - - plotMA - -gene-wise dispersion estimates - -mean-dispersion relationship - -final dispersion estimates - -you had estimated dispersions, replacing these - -gene-wise dispersion estimates - -mean-dispersion relationship - -final dispersion estimates - -you had estimated dispersions, replacing these - gene-wise dispersion estimates mean-dispersion relationship @@ -294,11 +232,11 @@ (Click on a thumbnail image to download the corresponding original PDF image)<br/> <div><table class="simple" cellpadding="2" cellspacing="2"> <tr> -<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" - alt="Image called VOOM_mean_variance_plot.pdf"/></a></td> +<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" + alt="Image called VOOM_DifferentialCounts_mean_variance_plot.pdf"/></a></td> -<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" - alt="Image called VOOM_qqplot.pdf"/></a></td> +<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" + alt="Image called VOOM_DifferentialCounts_qqplot.pdf"/></a></td> </tr> </table></div> @@ -309,107 +247,107 @@ # VOOM top 50 - ID logFC AveExpr t P.Value adj.P.Val B NReads URL + logFC AveExpr t P.Value adj.P.Val B NReads URL -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> </pre> @@ -418,28 +356,28 @@ (Click on a thumbnail image to download the corresponding original PDF image)<br/> <div><table class="simple" cellpadding="2" cellspacing="2"> <tr> -<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" - alt="Image called edgeR_BCV_vs_abundance.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_BCV_vs_abundance.pdf"/></a></td> -<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" - alt="Image called edgeR_GoodnessofFit.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_GoodnessofFit.pdf"/></a></td> -<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" - alt="Image called edgeR_MDSplot.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_MDSplot.pdf"/></a></td> </tr> <tr> -<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" - alt="Image called edgeR_qqplot.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_qqplot.pdf"/></a></td> -<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" - alt="Image called edgeR_raw_norm_counts_box.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_raw_norm_counts_box.pdf"/></a></td> -<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" - alt="Image called edgeR_smearplot.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_smearplot.pdf"/></a></td> </tr> <tr> -<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" - alt="Image called edgeR_top_100_heatmap.pdf"/></a></td> +<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" + alt="Image called edgeR_DifferentialCounts_top_100_heatmap.pdf"/></a></td> <td> </td><td> </td> </tr></table></div> @@ -448,19 +386,17 @@ <pre> -[1] prior.df = 8 +[1] Common Dispersion = 0.228651459675839 CV = 0.478175134940995 getPriorN = 3.33333333333333 [1] "No GLM fit outlier genes found\n" -[1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333 - -[1] heart liver +[1] Heart Liver [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365" [1] raw contig counts by sample: - liver_X11706Liv_CAAA liver_X11700Liv_ATTC liver_X11698Liv_ACTG liver_X11699Liv_ATGA heart_X11706He_AGTTC heart_X11699He_GGCTA heart_X11698He_TAGCT heart_X11700He_CTTGT + Liver_X11706Liv_CAAA Liver_X11700Liv_ATTC Liver_X11698Liv_ACTG Liver_X11699Liv_ATGA Heart_X11706He_AGTTC Heart_X11699He_GGCTA Heart_X11698He_TAGCT Heart_X11700He_CTTGT Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 @@ -478,7 +414,7 @@ [1] normalised contig counts by sample: - liver_X11706Liv_CAAA liver_X11700Liv_ATTC liver_X11698Liv_ACTG liver_X11699Liv_ATGA heart_X11706He_AGTTC heart_X11699He_GGCTA heart_X11698He_TAGCT heart_X11700He_CTTGT + Liver_X11706Liv_CAAA Liver_X11700Liv_ATTC Liver_X11698Liv_ACTG Liver_X11699Liv_ATGA Heart_X11706He_AGTTC Heart_X11699He_GGCTA Heart_X11698He_TAGCT Heart_X11700He_CTTGT Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf @@ -502,19 +438,19 @@ 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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> 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> @@ -522,21 +458,21 @@ 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> -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> +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> -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> +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> 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> 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> -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> +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> -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> +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> 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> -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> +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> 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> @@ -544,7 +480,7 @@ 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> -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> +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> 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> @@ -554,43 +490,43 @@ 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> -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> +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> -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> +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> 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> -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> +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> 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> 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> -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> +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> -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> +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> 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> 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> -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> +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> 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> 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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> -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> +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> 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> @@ -610,8 +546,8 @@ <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" alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td> -<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" - alt="Image called Venn_significant_genes_overlap.pdf"/></a></td> +<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" + alt="Image called Venn_DifferentialCounts_significant_genes_overlap.pdf"/></a></td> </tr> <tr> <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" @@ -638,19 +574,19 @@ [1] "@@ using genecards substitution for urls" -[1] # urls +[1] # urls sample [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> [6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a> -[1] # Total low count contigs per sample = 170,67,203,86,145,111,155,120 +[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 -[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 +[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 [1] Using design matrix: - (Intercept) groupliver + (Intercept) groupLiver 1 1 1 @@ -678,25 +614,25 @@ [1] contr.treatment -R version 3.0.1 (2013-05-16) +R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: - [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 + [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 attached base packages: - [1] parallel splines methods grid stats graphics grDevices utils datasets base +[1] parallel splines methods stats graphics grDevices utils datasets base other attached packages: - [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 + [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 loaded via a namespace (and not attached): - [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 + [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 </pre> @@ -705,28 +641,28 @@ <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr> -<tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.0 KB</td></tr> -<tr class="odd_row"><td><a href="DESeq2_MA_plot.pdf">DESeq2_MA_plot.pdf</a></td><td>14.7 KB</td></tr> -<tr><td><a href="DESeq2_PCA_plot.pdf">DESeq2_PCA_plot.pdf</a></td><td>4.9 KB</td></tr> -<tr class="odd_row"><td><a href="DESeq2_dispersion_estimates.pdf">DESeq2_dispersion_estimates.pdf</a></td><td>188.4 KB</td></tr> -<tr><td><a href="DESeq2_qqplot.pdf">DESeq2_qqplot.pdf</a></td><td>14.4 KB</td></tr> -<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> -<tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>27.1 KB</td></tr> -<tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>3.1 KB</td></tr> -<tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.2 KB</td></tr> +<tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr> +<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> +<tr><td><a href="DESeq2_DifferentialCounts_PCA_plot.pdf">DESeq2_DifferentialCounts_PCA_plot.pdf</a></td><td>4.9 KB</td></tr> +<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> +<tr><td><a href="DESeq2_DifferentialCounts_qqplot.pdf">DESeq2_DifferentialCounts_qqplot.pdf</a></td><td>12.8 KB</td></tr> +<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> +<tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>28.4 KB</td></tr> +<tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>2.0 KB</td></tr> +<tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.5 KB</td></tr> <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> -<tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr> -<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> -<tr><td><a href="VOOM_qqplot.pdf">VOOM_qqplot.pdf</a></td><td>17.6 KB</td></tr> -<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> +<tr><td><a href="VOOM.log">VOOM.log</a></td><td>9.4 KB</td></tr> +<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> +<tr><td><a href="VOOM_DifferentialCounts_qqplot.pdf">VOOM_DifferentialCounts_qqplot.pdf</a></td><td>17.5 KB</td></tr> +<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> <tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr> -<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> -<tr><td><a href="edgeR_GoodnessofFit.pdf">edgeR_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr> -<tr class="odd_row"><td><a href="edgeR_MDSplot.pdf">edgeR_MDSplot.pdf</a></td><td>4.9 KB</td></tr> -<tr><td><a href="edgeR_qqplot.pdf">edgeR_qqplot.pdf</a></td><td>15.2 KB</td></tr> -<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> -<tr><td><a href="edgeR_smearplot.pdf">edgeR_smearplot.pdf</a></td><td>16.6 KB</td></tr> -<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> +<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> +<tr><td><a href="edgeR_DifferentialCounts_GoodnessofFit.pdf">edgeR_DifferentialCounts_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr> +<tr class="odd_row"><td><a href="edgeR_DifferentialCounts_MDSplot.pdf">edgeR_DifferentialCounts_MDSplot.pdf</a></td><td>5.0 KB</td></tr> +<tr><td><a href="edgeR_DifferentialCounts_qqplot.pdf">edgeR_DifferentialCounts_qqplot.pdf</a></td><td>15.2 KB</td></tr> +<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> +<tr><td><a href="edgeR_DifferentialCounts_smearplot.pdf">edgeR_DifferentialCounts_smearplot.pdf</a></td><td>16.6 KB</td></tr> +<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> <tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr> </table></div><br/> </div></body></html>