Mercurial > repos > fubar > differential_count_models
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| author | fubar |
|---|---|
| date | Sun, 02 Mar 2014 23:08:26 -0500 |
| parents | c0fa3dde02d9 |
| children | 9f2e0ec3e826 |
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<!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/" /> <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="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_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_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> </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_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> </td> </tr></table></div> <div class="toolFormTitle">DESeq2 log output</div> <pre> # DESeq top 50 Contig baseMean log2FoldChange lfcSE 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 10.312083 0.3292695 2.649323e-215 1.479647e-212 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</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> 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> 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 -7.284200 0.3771119 3.959336e-83 7.370965e-81 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</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> 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> 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> 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> 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> 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> 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> 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 -8.059660 0.5142876 2.369067e-55 1.764165e-53 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</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> 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> 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> 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> 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> 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> 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> 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 -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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> </pre> <div class="toolFormTitle">DifferentialCounts log output</div> <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: splines Loading required package: DESeq2 Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following object is 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’: combine The following object is masked from ‘package:stats’: xtabs The following object is 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 Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:gplots’: 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: 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 final dispersion estimates Warning messages: 1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : Outlier (-Inf) in boxplot 1 is not drawn 2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : Outlier (-Inf) in boxplot 3 is not drawn 3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067, : some notches went outside hinges ('box'): maybe set notch=FALSE 4: In par(defpar) : calling par(new=TRUE) with no plot </pre> <div class="toolFormTitle">VOOM 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="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_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> </tr> </table></div> <div class="toolFormTitle">VOOM log output</div> <pre> # VOOM top 50 ID 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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 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> 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> 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> 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> 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> 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> 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 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> </pre> <div class="toolFormTitle">edgeR 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="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_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_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> </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_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_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> </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> </td><td> </td> </tr></table></div> <div class="toolFormTitle">edgeR log output</div> <pre> [1] prior.df = 8 [1] "No GLM fit outlier genes found\n" [1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333 [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 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 Min. :0.0043 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 Median :0.7789 Median :0.6031 Median :0.6998 Median :0.6031 Median :0.4786 Median :0.4786 Median :0.4786 Median :0.4786 Mean :1.0519 Mean :1.0343 Mean :0.9855 Mean :0.9966 Mean :0.9210 Mean :0.9428 Mean :1.0205 Mean :0.9753 3rd Qu.:1.5410 3rd Qu.:1.6335 3rd Qu.:1.4473 3rd Qu.:1.5534 3rd Qu.:1.5770 3rd Qu.:1.5855 3rd Qu.:1.7161 3rd Qu.:1.6022 Max. :5.8209 Max. :5.6905 Max. :5.7999 Max. :5.7215 Max. :5.3609 Max. :5.3589 Max. :5.6967 Max. :5.3702 NA's :650 NA's :969 NA's :664 NA's :886 NA's :902 NA's :957 NA's :821 NA's :950 [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 Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf 1st Qu.: 0 1st Qu.:-Inf 1st Qu.: 0 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Median : 0 Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf Mean :-Inf 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 3rd Qu.: 1 Max. : 6 Max. : 6 Max. : 6 Max. : 5 Max. : 5 Max. : 5 Max. : 6 Max. : 5 [1] Using ncol rawrs= 8 [1] # edgeR Top tags\n Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> 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> Snord91a Snord91a 2.654072 6.557504 62.40549 2.795431e-15 6.379174e-14 0.08637410 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a> [1] # 416 tags significant at adj p= 0.05 </pre> <div class="toolFormTitle">Other 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="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> </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" alt="Image called sample_counts_histogram.pdf"/></a></td> <td> </td> </tr></table></div> <div class="toolFormTitle">Other log output</div> <pre> ## Toolfactory generated command line = Rscript - None None Got TCols=1 5 6 7; CCols=2 3 4 8 [1] # Quantiles for non-zero row counts: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs [1] "@@ using genecards substitution for urls" [1] # urls [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] 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 1 1 1 2 1 1 3 1 1 4 1 1 5 1 0 6 1 0 7 1 0 8 1 0 attr(,"assign") [1] 0 1 attr(,"contrasts") attr(,"contrasts")$group [1] contr.treatment R version 3.0.1 (2013-05-16) 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 attached base packages: [1] parallel splines methods grid 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 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 </pre> <div class="toolFormTitle">All output files available for downloading</div> <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 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="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><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>