Mercurial > repos > fubar > differential_count_models
view rgedgeR/test-data/edgeRtest1out.html @ 9:2e35432ee040 draft
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| author | fubar |
|---|---|
| date | Sat, 27 Jul 2013 01:35:23 -0400 |
| parents | 2122e630b13a |
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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 "edgeR" run at 12/06/2013 16:42:51</div><br/> <div><table class="simple" cellpadding="2" cellspacing="2"> <tr> <td><a href="edgeRtest_BCV_vs_abundance.pdf"><img src="edgeRtest_BCV_vs_abundance.jpg" title="Click to download a PDF of edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400" alt="Image called edgeRtest_BCV_vs_abundance.pdf"/></a></td> <td><a href="edgeRtest_MDSplot.pdf"><img src="edgeRtest_MDSplot.jpg" title="Click to download a PDF of edgeRtest_MDSplot.pdf" hspace="5" width="400" alt="Image called edgeRtest_MDSplot.pdf"/></a></td> <td><a href="edgeRtest_RowsumCum.pdf"><img src="edgeRtest_RowsumCum.jpg" title="Click to download a PDF of edgeRtest_RowsumCum.pdf" hspace="5" width="400" alt="Image called edgeRtest_RowsumCum.pdf"/></a></td> </tr> <tr> <td><a href="edgeRtest_Smearplot.pdf"><img src="edgeRtest_Smearplot.jpg" title="Click to download a PDF of edgeRtest_Smearplot.pdf" hspace="5" width="400" alt="Image called edgeRtest_Smearplot.pdf"/></a></td> <td><a href="edgeRtest_heatmap.pdf"><img src="edgeRtest_heatmap.jpg" title="Click to download a PDF of edgeRtest_heatmap.pdf" hspace="5" width="400" alt="Image called edgeRtest_heatmap.pdf"/></a></td> <td><a href="edgeRtest_pval_qq.pdf"><img src="edgeRtest_pval_qq.jpg" title="Click to download a PDF of edgeRtest_pval_qq.pdf" hspace="5" width="400" alt="Image called edgeRtest_pval_qq.pdf"/></a></td> </tr> <tr> <td><a href="edgeRtest_sampleBoxplot.pdf"><img src="edgeRtest_sampleBoxplot.jpg" title="Click to download a PDF of edgeRtest_sampleBoxplot.pdf" hspace="5" width="400" alt="Image called edgeRtest_sampleBoxplot.pdf"/></a></td> <td><a href="edgeRtest_samplehistplot.pdf"><img src="edgeRtest_samplehistplot.jpg" title="Click to download a PDF of edgeRtest_samplehistplot.pdf" hspace="5" width="400" alt="Image called edgeRtest_samplehistplot.pdf"/></a></td> <td><a href="edgeRtest_venn.pdf"><img src="edgeRtest_venn.jpg" title="Click to download a PDF of edgeRtest_venn.pdf" hspace="5" width="400" alt="Image called edgeRtest_venn.pdf"/></a></td> </tr> <tr> <td><a href="edgeRtest_voomplot.pdf"><img src="edgeRtest_voomplot.jpg" title="Click to download a PDF of edgeRtest_voomplot.pdf" hspace="5" width="400" alt="Image called edgeRtest_voomplot.pdf"/></a></td> <td> </td><td> </td> </tr></table></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="edgeR.Rscript">edgeR.Rscript</a></td><td>19.7 KB)</td></tr> <tr class="odd_row"><td><a href="edgeR_runner.log">edgeR_runner.log</a></td><td>79.2 KB)</td></tr> <tr><td><a href="edgeRtest_BCV_vs_abundance.pdf">edgeRtest_BCV_vs_abundance.pdf</a></td><td>16.4 KB)</td></tr> <tr class="odd_row"><td><a href="edgeRtest_DESeq_TopTable.xls">edgeRtest_DESeq_TopTable.xls</a></td><td>135.1 KB)</td></tr> <tr><td><a href="edgeRtest_MDSplot.pdf">edgeRtest_MDSplot.pdf</a></td><td>4.9 KB)</td></tr> <tr class="odd_row"><td><a href="edgeRtest_RowsumCum.pdf">edgeRtest_RowsumCum.pdf</a></td><td>6.3 KB)</td></tr> <tr><td><a href="edgeRtest_Smearplot.pdf">edgeRtest_Smearplot.pdf</a></td><td>16.7 KB)</td></tr> <tr class="odd_row"><td><a href="edgeRtest_VOOM_topTable.xls">edgeRtest_VOOM_topTable.xls</a></td><td>131.4 KB)</td></tr> <tr><td><a href="edgeRtest_heatmap.pdf">edgeRtest_heatmap.pdf</a></td><td>11.3 KB)</td></tr> <tr class="odd_row"><td><a href="edgeRtest_pval_qq.pdf">edgeRtest_pval_qq.pdf</a></td><td>15.9 KB)</td></tr> <tr><td><a href="edgeRtest_sampleBoxplot.pdf">edgeRtest_sampleBoxplot.pdf</a></td><td>7.8 KB)</td></tr> <tr class="odd_row"><td><a href="edgeRtest_samplehistplot.pdf">edgeRtest_samplehistplot.pdf</a></td><td>10.9 KB)</td></tr> <tr><td><a href="edgeRtest_venn.pdf">edgeRtest_venn.pdf</a></td><td>9.7 KB)</td></tr> <tr class="odd_row"><td><a href="edgeRtest_voomplot.pdf">edgeRtest_voomplot.pdf</a></td><td>16.7 KB)</td></tr> </table></div><br/> <div class="toolFormTitle">Rscript log</div><pre> ## Toolfactory generated command line = Rscript - None /data/home/rlazarus/galaxy-central/database/files/000/dataset_2.dat 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(s) are masked from ‘package:stats’: nobs The following object(s) are 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(s) are masked from ‘package:stats’: lowess Loading required package: Biobase Loading required package: BiocGenerics Loading required package: methods Attaching package: ‘BiocGenerics’ The following object(s) are masked from ‘package:gdata’: combine The following object(s) are masked from ‘package:stats’: xtabs The following object(s) are masked from ‘package:base’: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: locfit locfit 1.5-9.1 2013-03-22 Loading required package: lattice Warning message: found methods to import for function ‘eapply’ but not the generic itself Loading required package: limma Attaching package: ‘limma’ The following object(s) are masked from ‘package:DESeq’: plotMA # got TCols=2 3 4 8; CCols=1 5 6 7 [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] # Total low count contigs per sample = 145,111,155,120,170,67,203,86 Calculating library sizes from column totals. [1] Using samples: case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam,control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam [1] Using design matrix: (Intercept) groupcase 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 [1] "No GLM fit outlier genes found\n" [1] Common Dispersion = 0.24088423096811 CV = 0.490799583300669 getPriorN = 3.33333333333333 [1] "Raw sample read totals 1440960,1341813,2888924,1428365,2443751,1644652,1682104,1806045" [1] raw contig counts by sample: case_X11706He_AGTTCC case_X11699He_GGCTAC case_X11698He_TAGCTT case_X11700He_CTTGTA control_X11706Liv_CA control_X11700Liv_AT control_X11698Liv_AC control_X11699Liv_AT 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.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.0043 1st Qu.:0.3032 1st Qu.:0.0043 1st Qu.:0.3032 1st Qu.:0.0043 Median :0.4786 Median :0.4786 Median :0.4786 Median :0.4786 Median :0.7789 Median :0.6031 Median :0.6998 Median :0.6031 Mean :0.9210 Mean :0.9428 Mean :1.0205 Mean :0.9753 Mean :1.0519 Mean :1.0343 Mean :0.9855 Mean :0.9966 3rd Qu.:1.5770 3rd Qu.:1.5855 3rd Qu.:1.7161 3rd Qu.:1.6022 3rd Qu.:1.5410 3rd Qu.:1.6335 3rd Qu.:1.4473 3rd Qu.:1.5534 Max. :5.3609 Max. :5.3589 Max. :5.6967 Max. :5.3702 Max. :5.8209 Max. :5.6905 Max. :5.7999 Max. :5.7215 NA's :902 NA's :957 NA's :821 NA's :950 NA's :650 NA's :969 NA's :664 NA's :886 [1] normalised contig counts by sample: case_X11706He_AGTTCC case_X11699He_GGCTAC case_X11698He_TAGCTT case_X11700He_CTTGTA control_X11706Liv_CA control_X11700Liv_AT control_X11698Liv_AC control_X11699Liv_AT Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf Min. :-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.:-Inf 1st Qu.: 0 1st Qu.:-Inf 1st Qu.: 0 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. : 5 Max. : 5 Max. : 6 Max. : 5 Max. : 6 Max. : 6 Max. : 6 Max. : 5 [1] Using ncol rawrs= 8 [1] # writing output [1] # urls <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'></a>0610005C13Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'></a>0610007N19Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'></a>0610008F07Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'></a>0610009L18Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'></a>0610012G03Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'></a>0610031O16Rik</a># Top tags Name logFC logCPM LR PValue adj.p.value Dispersion totreads case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam Mir122a Mir122a -10.661348 12.537949 445.91203 5.594743e-99 6.383602e-96 0.10205510 90428 6.644669 2.864648e+00 2.012369e+01 4.756523e+00 2.084166e+04 1.681895e+04 Mir192 Mir192 -7.109019 17.247415 366.13166 1.301558e-81 7.425390e-79 0.07765487 2325567 1779.663879 1.294412e+03 4.493546e+03 1.933526e+03 4.635990e+05 3.403123e+05 Mir208b Mir208b 13.423720 9.822338 355.41782 2.801296e-79 1.065426e-76 0.12444059 14756 1245.907022 5.701390e+02 4.930344e+03 8.819024e+02 7.453220e-01 0.000000e+00 Mir208a Mir208a 11.977586 8.388290 348.81540 7.675451e-78 2.189422e-75 0.09936798 4638 433.789590 7.125278e+02 1.006599e+03 6.497485e+02 0.000000e+00 0.000000e+00 Mir499 Mir499 14.488216 8.612770 291.12794 2.823507e-65 6.443244e-63 0.13481620 6527 608.439028 5.066577e+02 2.521609e+03 2.703574e+02 0.000000e+00 0.000000e+00 Mir149 Mir149 6.869731 8.785665 253.01986 5.702930e-57 1.084507e-54 0.09834684 6164 774.657675 4.595714e+02 1.710514e+03 7.663947e+02 1.750400e+01 6.246465e+00 Mir490 Mir490 8.453930 6.909596 251.05610 1.528281e-56 2.491098e-54 0.09745005 1741 209.881557 2.177498e+02 5.205387e+02 1.957941e+02 1.038505e+00 5.537224e-01 Mir802 Mir802 -12.499678 6.629391 237.56161 1.337812e-53 1.908055e-51 0.10939981 1514 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 3.056548e+02 1.641034e+02 Mir204 Mir204 7.371179 7.558996 237.12302 1.667365e-53 2.113848e-51 0.10292005 2601 425.578854 3.264164e+02 6.462477e+02 3.754819e+02 3.040281e+00 6.923364e-01 Mir1948 Mir1948 -7.583326 7.293456 204.79641 1.875897e-46 2.140399e-44 0.11833999 2404 1.216112 6.923364e-01 1.661167e+00 1.636942e+00 6.476848e+02 3.852783e+02 Mir3073 Mir3073 -11.748556 5.881462 200.03350 2.053625e-45 2.130170e-43 0.11068562 904 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 2.073471e+02 7.546467e+01 Mir194-2 Mir194-2 -5.439827 7.860048 165.57239 6.859199e-38 6.521955e-36 0.10671020 3570 10.520726 6.138532e+00 1.490644e+01 9.513045e+00 9.214105e+02 6.003547e+02 Mir10b Mir10b 5.032898 13.880770 160.06580 1.094640e-36 9.607570e-35 0.10795434 197340 25838.822630 3.216361e+04 3.631730e+04 3.446522e+04 1.825385e+03 3.738617e+02 Mir101b Mir101b -3.925287 11.936090 120.62427 4.618143e-28 3.763787e-26 0.09663075 59019 219.816815 3.012250e+02 8.119232e+02 4.270695e+02 1.014507e+04 7.747970e+03 Mir182 Mir182 -5.244384 8.942708 118.92815 1.085926e-27 8.260276e-26 0.14993443 7189 16.962242 1.439678e+01 2.209871e+01 3.130352e+01 9.840056e+02 6.154406e+02 Mir200b Mir200b -6.725348 5.765187 115.73189 5.440989e-27 3.880105e-25 0.16712490 888 2.432225 0.000000e+00 1.661167e+00 0.000000e+00 3.696797e+02 9.750871e+01 Mir181c Mir181c 3.611867 10.569815 107.82011 2.943153e-25 1.975375e-23 0.09385270 23605 2420.852087 1.892879e+03 4.093093e+03 1.902590e+03 2.320365e+02 2.727878e+02 Mir181d Mir181d 3.489976 7.232064 102.18661 5.053019e-24 3.203053e-22 0.08738498 2139 310.053946 2.021522e+02 5.398233e+02 2.956660e+02 3.648337e+01 1.453906e+01 Mir21 Mir21 -3.077771 13.881500 91.37324 1.189745e-21 7.144733e-20 0.08494272 229120 3207.212585 2.190826e+03 4.348911e+03 2.010566e+03 2.715400e+04 3.322794e+04 Mir199b Mir199b 5.411476 4.695869 86.70372 1.260596e-20 7.191701e-19 0.15656183 370 43.403268 4.481024e+01 9.924938e+01 4.925255e+01 1.384673e+00 5.537224e-01 Mir193 Mir193 -5.360157 4.775477 84.66127 3.541205e-20 1.924055e-18 0.15546497 421 1.490644 1.189131e+00 2.800640e+00 6.940516e-01 1.015454e+02 3.496299e+01 Mir23a Mir23a 3.003071 9.467420 82.28684 1.177029e-19 6.104501e-18 0.08920345 10118 1149.889322 1.127958e+03 2.471518e+03 1.096325e+03 1.505832e+02 1.268024e+02 Mir195 Mir195 3.060546 8.152797 81.39727 1.846126e-19 9.158392e-18 0.09133016 3962 429.134881 2.831909e+02 9.227086e+02 4.708957e+02 1.106253e+02 7.773378e+01 Ahsg Ahsg -10.101343 6.638589 79.82133 4.098447e-19 1.923759e-17 0.42092199 1524 0.000000 5.537224e-01 0.000000e+00 0.000000e+00 3.484153e+02 1.260288e+01 Mir148a Mir148a -2.789375 16.047169 79.76589 4.215073e-19 1.923759e-17 0.08196054 1002397 15925.598251 8.528200e+03 2.207082e+04 1.059020e+04 1.927239e+05 1.054456e+05 Dnm3os Dnm3os 3.189443 6.618834 79.19614 5.623979e-19 2.468062e-17 0.09496531 1401 134.000827 8.716715e+01 3.652078e+02 1.825316e+02 3.710848e+01 2.498586e+01 Mir27a Mir27a 2.921772 10.581277 77.26988 1.491231e-18 6.301832e-17 0.09125059 21886 2383.612353 2.512174e+03 5.321988e+03 2.361690e+03 3.285136e+02 3.477377e+02 Mir429 Mir429 -5.341934 4.951103 76.38758 2.331128e-18 9.499346e-17 0.18324117 499 1.783696 7.001600e-01 2.082155e+00 1.824168e+00 9.173458e+01 4.540524e+01 Mir214 Mir214 3.125906 6.202347 74.28213 6.771387e-18 2.664191e-16 0.09532762 1048 110.058161 5.642542e+01 1.982326e+02 9.371492e+01 3.353949e+01 1.545870e+01 Mir200a Mir200a -7.592263 4.059943 73.71426 9.028450e-18 3.433821e-16 0.22417820 264 0.000000 0.000000e+00 5.945653e-01 0.000000e+00 9.022671e+01 3.222698e+01 Mir194-1 Mir194-1 -3.970219 5.393899 73.22380 1.157517e-17 4.260408e-16 0.13095886 635 3.567392 9.102080e+00 5.552413e+00 3.648337e+00 7.615701e+01 8.859559e+01 Mir378 Mir378 2.954320 8.053368 73.09647 1.234655e-17 4.402315e-16 0.09566655 4075 425.697272 3.921392e+02 1.155915e+03 1.883155e+02 7.641369e+01 3.683119e+01 Mir322 Mir322 3.058569 8.948242 72.83721 1.407969e-17 4.868160e-16 0.10365695 7074 1012.892580 6.718588e+02 1.784708e+03 8.550716e+02 1.587027e+02 7.892635e+01 Mir215 Mir215 2.908934 6.381924 70.31105 5.065317e-17 1.699861e-15 0.09002036 1182 123.075020 1.610368e+02 2.727623e+02 1.222193e+02 1.938542e+01 1.716540e+01 Cyp3a25 Cyp3a25 -9.778602 3.913257 70.02642 5.851533e-17 1.907600e-15 0.26445237 226 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 5.664447e+01 1.783696e+01 Mir183 Mir183 -4.214462 5.247929 66.31101 3.851010e-16 1.220556e-14 0.15955164 563 8.401920 1.388103e+00 2.432225e+00 2.423177e+00 8.638070e+01 2.905572e+01 Mir181a-2 Mir181a-2 2.837713 7.573798 65.52900 5.726500e-16 1.765929e-14 0.09834030 2817 288.826664 1.377749e+02 6.395494e+02 1.821098e+02 5.813511e+01 4.102501e+01 Mir155 Mir155 3.734310 4.975364 65.07600 7.206449e-16 2.163831e-14 0.13295455 463 33.966543 5.888044e+01 1.141565e+02 5.251200e+01 9.716723e+00 1.824168e+00 Snord91a Snord91a -2.818342 6.592251 64.29345 1.072014e-15 3.136329e-14 0.09422446 1437 13.846728 1.605795e+01 3.314807e+01 1.863305e+01 2.158272e+02 1.792410e+02 Mir125b-2 Mir125b-2 2.852233 8.081093 64.20822 1.119409e-15 3.193115e-14 0.10276578 3837 315.520541 4.404853e+02 7.634219e+02 4.852109e+02 1.082721e+02 9.060036e+01 Serpina4-ps1 Serpina4-ps1 -10.090564 4.224051 64.02094 1.231040e-15 3.425894e-14 0.34406452 295 0.000000 0.000000e+00 0.000000e+00 0.000000e+00 1.080717e+02 1.129674e+01 Mir133b Mir133b 9.293392 3.404704 63.59576 1.527577e-15 4.149919e-14 0.26404392 159 17.719118 1.064012e+01 5.738979e+01 1.426957e+01 0.000000e+00 0.000000e+00 Gm10069 Gm10069 -7.475459 6.400326 63.15445 1.911172e-15 5.071271e-14 0.41541432 1309 1.189131 1.400320e+00 6.940516e-01 6.080561e-01 1.914310e+02 6.644669e+00 Mir871 Mir871 -5.633588 4.283233 62.67513 2.437746e-15 6.321517e-14 0.21907826 290 1.227706 7.453220e-01 5.945653e-01 0.000000e+00 5.691223e+01 4.925255e+01 Mir184 Mir184 5.002968 4.123691 61.97642 3.475940e-15 8.813439e-14 0.19289992 247 33.443087 1.419290e+01 4.983502e+01 2.168948e+01 2.981288e+00 0.000000e+00 Mir132 Mir132 2.702863 5.866134 58.80773 1.738573e-14 4.312416e-13 0.09148478 857 82.695634 4.327103e+01 1.821747e+02 6.097608e+01 2.832224e+01 1.308044e+01 Snord104 Snord104 -2.492063 11.108871 58.55547 1.976394e-14 4.798012e-13 0.09093023 33458 614.929745 4.378004e+02 8.629974e+02 5.144081e+02 3.826761e+03 4.181256e+03 Mir3074-2 Mir3074-2 2.635505 7.871042 57.72938 3.007773e-14 7.149726e-13 0.09900198 3470 450.903031 3.206519e+02 8.354691e+02 1.716994e+02 8.970303e+01 5.197290e+01 Mir24-2 Mir24-2 2.635505 7.871042 57.68174 3.081509e-14 7.175515e-13 0.09908656 3470 479.987359 2.746892e+02 9.620198e+02 3.442496e+02 9.850509e+01 4.396336e+01 5430416N02Rik 5430416N02Rik -3.267228 5.202367 56.75137 4.945455e-14 1.128553e-12 0.12456687 564 6.080561 1.730841e+00 1.273562e+01 4.910826e+00 1.453378e+02 5.886197e+01 control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam Mir122a 7.242557e+03 8.468313e+03 12 7 27 8 29767 Mir192 3.835916e+05 1.822922e+05 3214 3163 6029 3252 662133 Mir208b 0.000000e+00 0.000000e+00 2049 1647 8904 2155 1 Mir208a 0.000000e+00 5.537224e-01 1060 956 1693 928 0 Mir499 0.000000e+00 0.000000e+00 869 730 4147 781 0 Mir149 4.864449e+00 5.538691e+00 1399 1123 2295 1289 25 Mir490 0.000000e+00 7.453220e-01 353 311 750 322 3 Mir802 1.557723e+02 2.092870e+02 0 0 0 0 552 Mir204 5.537224e-01 3.683119e+00 571 549 923 541 5 Mir1948 1.813414e+02 4.282299e+02 2 2 3 4 869 Mir3073 7.253764e+01 8.757639e+01 0 0 0 0 341 Mir194-2 2.669366e+02 3.046280e+02 19 15 20 16 1316 Mir10b 6.583760e+02 7.272114e+02 34668 54096 51870 49658 3002 Mir101b 1.128042e+04 6.628420e+03 635 544 1984 573 17063 Mir182 2.366022e+03 6.536603e+02 49 26 54 42 1655 Mir200b 4.621056e+01 1.075780e+02 4 0 3 0 496 Mir181c 2.283131e+02 2.989683e+02 3488 3113 11824 3436 567 Mir181d 2.547123e+01 1.555095e+01 416 340 771 426 60 Mir21 2.570722e+04 3.537908e+04 4621 3603 12563 3631 66353 Mir199b 0.000000e+00 2.981288e+00 73 64 143 81 4 Mir193 3.377707e+01 3.396654e+01 2 2 4 1 167 Mir23a 8.921333e+01 2.437203e+02 1934 1611 3561 1803 435 Mir195 4.560421e+01 4.154019e+01 775 692 1238 792 158 Ahsg 6.100714e+02 2.432225e+01 0 1 0 0 586 Mir148a 1.795497e+05 1.342747e+05 26191 24636 39859 25878 258578 Dnm3os 1.216112e+01 1.384673e+01 242 213 490 307 53 Mir27a 1.636942e+02 5.664447e+02 4009 3588 7668 3884 949 Mir429 1.677865e+01 7.527752e+01 3 1 3 3 265 Mir214 1.190272e+01 2.012750e+01 181 163 358 229 45 Mir200a 1.142355e+01 2.602495e+01 0 0 1 0 130 Mir194-1 3.314807e+01 1.050904e+02 6 13 8 6 220 Mir378 9.167460e+01 6.302392e+01 608 565 1901 544 138 Mir322 5.038874e+01 9.166874e+01 1359 1130 2549 1232 261 Mir215 1.145859e+01 2.683159e+01 207 230 393 201 56 Cyp3a25 6.511488e+01 1.873939e+01 0 0 0 0 76 Mir183 1.349033e+02 7.729349e+01 12 2 4 7 156 Mir181a-2 8.051840e+01 5.691223e+01 475 398 1155 445 78 Mir155 2.769346e+00 4.983502e+00 83 79 192 75 14 Snord91a 2.484705e+02 1.732960e+02 40 29 81 25 363 Mir125b-2 2.077009e+01 7.364508e+01 771 591 1284 693 156 Serpina4-ps1 8.191872e+01 9.716723e+00 0 0 0 0 145 Mir133b 0.000000e+00 0.000000e+00 32 26 77 24 0 Gm10069 2.868741e+02 2.757691e+01 2 2 1 1 553 Mir871 1.003888e+01 5.149619e+01 3 1 1 0 82 Mir184 1.400320e+00 1.388103e+00 55 41 90 53 4 Mir132 2.100480e+01 1.943345e+01 136 125 329 149 38 Snord104 4.430701e+03 4.212863e+03 886 720 2493 929 9351 Mir3074-2 4.844593e+01 8.323914e+01 644 462 1374 496 162 Mir24-2 3.599196e+01 5.729296e+01 644 462 1374 496 162 5430416N02Rik 5.531264e+01 9.786128e+01 10 5 23 12 195 control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam ntotreads URL Mir122a 24233 11911 24463 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'></a>Mir122a</a> Mir192 490327 630849 526600 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'></a>Mir192</a> Mir208b 0 0 0 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'></a>Mir208b</a> Mir208a 0 0 1 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'></a>Mir208a</a> Mir499 0 0 0 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'></a>Mir499</a> Mir149 9 8 16 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'></a>Mir149</a> Mir490 1 0 1 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'></a>Mir490</a> Mir802 401 209 352 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'></a>Mir802</a> Mir204 2 1 9 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'></a>Mir204</a> Mir1948 648 259 617 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'></a>Mir1948</a> Mir3073 218 131 214 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'></a>Mir3073</a> Mir194-2 865 439 880 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'></a>Mir194-2</a> Mir10b 1080 1189 1777 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'></a>Mir10b</a> Mir101b 11066 16253 10901 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'></a>Mir101b</a> Mir182 879 3409 1075 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'></a>Mir182</a> Mir200b 164 66 155 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'></a>Mir200b</a> Mir181c 366 384 427 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'></a>Mir181c</a> Mir181d 42 46 38 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'></a>Mir181d</a> Mir21 44582 43237 50530 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'></a>Mir21</a> Mir199b 1 0 4 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'></a>Mir199b</a> Mir193 101 61 83 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'></a>Mir193</a> Mir23a 229 218 327 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'></a>Mir23a</a> Mir195 112 75 120 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'></a>Mir195</a> Ahsg 18 879 40 1524 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ahsg'></a>Ahsg</a> Mir148a 177349 256441 193465 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'></a>Mir148a</a> Dnm3os 36 20 40 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'></a>Dnm3os</a> Mir27a 628 400 760 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'></a>Mir27a</a> Mir429 82 41 101 499 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir429'></a>Mir429</a> Mir214 26 17 29 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'></a>Mir214</a> Mir200a 53 33 47 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'></a>Mir200a</a> Mir194-1 160 81 141 635 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'></a>Mir194-1</a> Mir378 90 123 106 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'></a>Mir378</a> Mir322 228 91 224 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'></a>Mir322</a> Mir215 31 28 36 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'></a>Mir215</a> Cyp3a25 30 93 27 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'></a>Cyp3a25</a> Mir183 71 181 130 563 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir183'></a>Mir183</a> Mir181a-2 69 115 82 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'></a>Mir181a-2</a> Mir155 3 8 9 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'></a>Mir155</a> Snord91a 256 358 285 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'></a>Snord91a</a> Mir125b-2 149 60 133 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'></a>Mir125b-2</a> Serpina4-ps1 19 117 14 295 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Serpina4-ps1'></a>Serpina4-ps1</a> Mir133b 0 0 0 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'></a>Mir133b</a> Gm10069 12 701 37 1309 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10069'></a>Gm10069</a> Mir871 81 29 93 290 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir871'></a>Mir871</a> Mir184 0 2 2 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'></a>Mir184</a> Mir132 22 30 28 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'></a>Mir132</a> Snord104 5610 7452 6017 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'></a>Snord104</a> Mir3074-2 127 65 140 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'></a>Mir3074-2</a> Mir24-2 127 65 140 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'></a>Mir24-2</a> 5430416N02Rik 99 79 141 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'></a>5430416N02Rik</a> [1] # 445 tags significant at adj p= 0.05 [1] # deTags [1] "0610005C13Rik" "0610007N19Rik" "0610008F07Rik" "0610012G03Rik" "0610031O16Rik" "1110038B12Rik" # DESeq top 50 id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj 536 Mir122a 10112.31117 2.021162e+04 1.300527e+01 6.434550e-04 -10.601873 5.488369e-57 6.262229e-54 645 Mir208a 616.76981 2.430915e-01 1.233297e+03 5.073385e+03 12.308733 6.046036e-53 3.449263e-50 600 Mir192 271352.97636 5.385927e+05 4.113233e+03 7.637001e-03 -7.032778 1.311798e-38 4.989204e-36 568 Mir149 810.35429 1.224267e+01 1.608466e+03 1.313819e+02 7.037623 7.073079e-37 2.017596e-34 791 Mir490 220.99790 9.450198e-01 4.410508e+02 4.667107e+02 8.866385 1.354865e-36 3.091803e-34 642 Mir204 347.57397 3.737736e+00 6.914102e+02 1.849810e+02 7.531234 8.058436e-36 1.532446e-33 844 Mir802 166.83414 3.336683e+02 0.000000e+00 0.000000e+00 -Inf 3.255469e-35 5.306414e-33 698 Mir3073 98.93199 1.978640e+02 0.000000e+00 0.000000e+00 -Inf 1.111351e-28 1.585065e-26 646 Mir208b 1649.77924 1.445675e-01 3.299414e+03 2.282265e+04 14.478178 7.505934e-28 9.515857e-26 614 Mir1948 263.89527 5.246983e+02 3.092210e+00 5.893310e-03 -7.406706 1.534188e-26 1.750509e-24 608 Mir194-2 391.65678 7.637703e+02 1.954329e+01 2.558791e-02 -5.288394 1.622682e-24 1.683163e-22 796 Mir499 712.45950 0.000000e+00 1.424919e+03 Inf Inf 2.577318e-19 2.450600e-17 585 Mir181c 2765.96510 3.955399e+02 5.136390e+03 1.298577e+01 3.698860 1.942959e-17 1.705320e-15 631 Mir199b 47.84725 1.818862e+00 9.387565e+01 5.161231e+01 5.689643 4.012622e-15 3.270287e-13 530 Mir10b 27820.40551 1.501200e+03 5.413961e+04 3.606421e+01 5.172496 3.069912e-14 2.335180e-12 586 Mir181d 275.22797 4.254569e+01 5.079103e+02 1.193800e+01 3.577489 5.204519e-14 3.711473e-12 602 Mir193 45.70861 8.913819e+01 2.279021e+00 2.556728e-02 -5.289558 1.657854e-13 1.112713e-11 637 Mir200a 27.09009 5.402561e+01 1.545578e-01 2.860824e-03 -8.449354 2.466964e-13 1.563781e-11 722 Mir322 899.53469 1.797868e+02 1.619283e+03 9.006682e+00 3.170996 1.359804e-12 8.165978e-11 756 Mir378 483.21548 1.056050e+02 8.608260e+02 8.151374e+00 3.027043 2.046396e-12 1.160965e-10 523 Mir101b 6846.19683 1.280838e+04 8.840090e+02 6.901800e-02 -3.856884 2.136745e-12 1.160965e-10 552 Mir133b 19.46050 0.000000e+00 3.892101e+01 Inf Inf 2.388227e-12 1.238621e-10 663 Mir23a 1289.18043 2.671574e+02 2.311203e+03 8.651093e+00 3.112882 3.093049e-12 1.534421e-10 671 Mir27a 2788.72629 6.066392e+02 4.970813e+03 8.194019e+00 3.034571 5.970859e-12 2.838646e-10 616 Mir195 519.86200 1.038507e+02 9.358733e+02 9.011721e+00 3.171803 6.245320e-12 2.850364e-10 607 Mir194-1 71.10636 1.325374e+02 9.675354e+00 7.300095e-02 -3.775941 1.405195e-11 6.166645e-10 344 Dnm3os 179.61643 3.285433e+01 3.263785e+02 9.934110e+00 3.312391 1.503324e-11 6.352936e-10 590 Mir184 32.23796 1.645700e+00 6.283021e+01 3.817841e+01 5.254685 1.644760e-11 6.702396e-10 582 Mir181a-2 347.82506 8.313904e+01 6.125111e+02 7.367310e+00 2.881138 2.735424e-11 1.076248e-09 541 Mir125b-2 493.08516 1.122867e+02 8.738836e+02 7.782608e+00 2.960254 5.662328e-11 2.153572e-09 573 Mir155 57.66182 7.341434e+00 1.079822e+02 1.470860e+01 3.878588 6.173765e-11 2.272344e-09 464 Gm5441 20.24317 2.430915e-01 4.024325e+01 1.655478e+02 7.371104 6.503611e-11 2.318944e-09 571 Mir153 19.90411 2.430915e-01 3.956513e+01 1.627582e+02 7.346586 8.675688e-11 2.999685e-09 649 Mir21 26121.31011 4.639963e+04 5.842995e+03 1.259276e-01 -2.989333 1.048681e-10 3.519252e-09 654 Mir214 134.69038 2.546966e+01 2.439111e+02 9.576536e+00 3.259504 1.338023e-10 4.361954e-09 638 Mir200b 87.13638 1.725548e+02 1.717931e+00 9.955853e-03 -6.650239 2.397950e-10 7.600169e-09 666 Mir24-2 424.48288 1.104079e+02 7.385578e+02 6.689355e+00 2.741867 4.542021e-10 1.363802e-08 700 Mir3074-2 424.48288 1.104079e+02 7.385578e+02 6.689355e+00 2.741867 4.542021e-10 1.363802e-08 845 Mir871 33.03360 6.461640e+01 1.450790e+00 2.245235e-02 -5.476990 5.839129e-10 1.708320e-08 767 Mir429 49.75018 9.677270e+01 2.727653e+00 2.818618e-02 -5.148868 6.903556e-10 1.969239e-08 655 Mir215 152.78082 3.329953e+01 2.722621e+02 8.176156e+00 3.031423 8.994273e-10 2.503040e-08 566 Mir148a 118994.46955 2.065090e+05 3.147993e+04 1.524386e-01 -2.713700 1.022762e-09 2.772155e-08 569 Mir150 553.20599 1.318948e+02 9.745171e+02 7.388592e+00 2.885299 1.044721e-09 2.772155e-08 628 Mir1983 14.04997 0.000000e+00 2.809994e+01 Inf Inf 2.859722e-09 7.415778e-08 581 Mir181a-1 59.53826 1.179305e+01 1.072835e+02 9.097179e+00 3.185419 3.537731e-09 8.970115e-08 784 Mir470 18.37716 3.608521e+01 6.691037e-01 1.854232e-02 -5.753034 7.467127e-09 1.852172e-07 630 Mir199a-2 44.84878 7.384673e+00 8.231288e+01 1.114645e+01 3.478512 8.433815e-09 2.047443e-07 550 Mir132 106.46062 2.691980e+01 1.860014e+02 6.909467e+00 2.788574 1.329950e-08 3.161402e-07 76 2610203C20Rik 79.17666 1.649993e+01 1.418534e+02 8.597210e+00 3.103869 1.594438e-08 3.712764e-07 540 Mir125b-1 79.01988 1.649993e+01 1.415398e+02 8.578206e+00 3.100676 1.650666e-08 3.766821e-07 # VOOM top 50 ID logFC AveExpr t P.Value adj.P.Val B 600 Mir192 -6.948883 14.6763803 -42.722954 2.301199e-16 2.625668e-13 27.266471 536 Mir122a -10.426125 8.1698641 -21.722912 2.859682e-12 1.087633e-09 17.760171 568 Mir149 7.030463 6.3160807 20.883835 4.915491e-12 1.402144e-09 17.277609 645 Mir208a 11.015018 3.9395538 23.252407 1.118938e-12 6.383542e-10 17.208662 530 Mir10b 5.130915 12.2628672 18.242023 3.124991e-11 4.963978e-09 16.221503 561 Mir143hg 2.249221 16.2444825 18.082481 3.521739e-11 4.963978e-09 16.026695 560 Mir143 2.251067 16.2358599 18.081481 3.524391e-11 4.963978e-09 16.026084 646 Mir208b 12.433228 4.6076218 19.592458 1.179199e-11 2.690931e-09 15.683666 523 Mir101b -3.765722 10.8508440 -16.538566 1.180419e-10 1.036045e-08 14.900027 796 Mir499 11.567529 3.7874598 17.942086 3.915496e-11 4.963978e-09 14.821741 566 Mir148a -2.638213 15.4435820 -16.548188 1.171186e-10 1.036045e-08 14.814792 844 Mir802 -9.158434 2.9157675 -17.316522 6.338616e-11 7.232360e-09 14.381577 698 Mir3073 -8.420542 2.5457189 -16.702657 1.033066e-10 1.036045e-08 13.985845 649 Mir21 -2.938537 13.1642917 -15.375404 3.148335e-10 2.394833e-08 13.867698 585 Mir181c 3.742560 9.6295577 15.242361 3.537063e-10 2.522368e-08 13.810405 791 Mir490 8.474378 3.7506957 16.259650 1.484816e-10 1.210125e-08 13.424617 663 Mir23a 3.165768 8.7896592 14.631179 6.110682e-10 3.873493e-08 13.269174 586 Mir181d 3.636211 6.3713218 14.317073 8.157508e-10 4.898798e-08 12.956333 642 Mir204 7.684425 4.7751735 15.033484 4.254268e-10 2.855364e-08 12.822427 671 Mir27a 3.106935 9.9255796 13.838251 1.281011e-09 6.960160e-08 12.513086 552 Mir133b 6.493549 1.2544862 13.969968 1.129934e-09 6.446275e-08 11.982684 608 Mir194-2 -5.264136 6.0897615 -13.044012 2.792884e-09 1.448491e-07 11.715753 616 Mir195 3.216595 7.4509350 12.869478 3.332788e-09 1.653353e-07 11.587523 756 Mir378 3.097393 7.3832049 11.684163 1.171371e-08 5.346138e-07 10.329692 672 Mir27b 1.976376 15.0957731 11.756036 1.082197e-08 5.144946e-07 10.127719 1017 Snord104 -2.337374 10.6109024 -11.495675 1.444482e-08 6.339052e-07 10.023395 722 Mir322 3.296618 8.2153415 11.415362 1.580762e-08 6.441605e-07 10.008472 655 Mir215 3.045873 5.7544234 11.148134 2.141822e-08 8.082459e-07 9.753268 628 Mir1983 5.895500 0.9931851 11.445812 1.527548e-08 6.441605e-07 9.749260 344 Dnm3os 3.363344 5.8607432 11.092261 2.283960e-08 8.082459e-07 9.689496 637 Mir200a -6.191561 1.7981309 -11.322172 1.756229e-08 6.909853e-07 9.662295 587 Mir182 -4.903995 7.1511683 -11.074468 2.331304e-08 8.082459e-07 9.658842 582 Mir181a-2 3.048298 6.9414651 11.072128 2.337609e-08 8.082459e-07 9.644017 614 Mir1948 -7.195525 4.5513493 -11.005492 2.524936e-08 8.473388e-07 9.341794 654 Mir214 3.280874 5.4784451 10.768257 3.332555e-08 1.086413e-06 9.318504 571 Mir153 5.963803 1.4386315 10.727082 3.498742e-08 1.093990e-06 9.035569 318 Cyp3a25 -6.318200 1.4888933 -10.698226 3.620443e-08 1.093990e-06 9.024973 464 Gm5441 5.982176 1.4484953 10.692891 3.643436e-08 1.093990e-06 9.000362 541 Mir125b-2 3.077678 7.4316058 10.446668 4.893073e-08 1.431538e-06 8.884250 551 Mir133a-1 5.144671 0.5903264 10.358205 5.447229e-08 1.553822e-06 8.575535 550 Mir132 2.847559 5.3211839 10.110952 7.380297e-08 2.004981e-06 8.531491 13 1110038B12Rik -2.226702 10.8487089 -10.194609 6.655312e-08 1.852125e-06 8.439308 922 Rabggtb -1.935779 9.9874171 -9.928995 9.262821e-08 2.457879e-06 8.133384 569 Mir150 2.938531 7.6297870 9.842102 1.033602e-07 2.620755e-06 8.116464 800 Mir504 5.256127 0.6221088 9.892894 9.693595e-08 2.513725e-06 8.068853 573 Mir155 3.906600 3.9899000 9.732173 1.188627e-07 2.712448e-06 8.046518 666 Mir24-2 2.833979 7.3083691 9.767192 1.136724e-07 2.646944e-06 8.030550 700 Mir3074-2 2.833979 7.3083691 9.767192 1.136724e-07 2.646944e-06 8.030550 664 Mir23b 2.124129 9.8141190 9.806316 1.081569e-07 2.625681e-06 7.979464 631 Mir199b 5.752816 2.8805143 9.823920 1.057683e-07 2.623514e-06 7.979387 Warning messages: 1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : Outlier (-Inf) in boxplot 5 is not drawn 2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group == : Outlier (-Inf) in boxplot 7 is not drawn 3: In bxp(list(stats = c(-Inf, -Inf, -0.158608221176912, 0.826586442285183, : some notches went outside hinges ('box'): maybe set notch=FALSE 4: In par(defpar) : calling par(new=TRUE) with no plot R version 2.15.1 (2012-06-22) 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] methods grid stats graphics grDevices utils datasets base other attached packages: [1] edgeR_3.0.8 limma_3.14.4 DESeq_1.10.1 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.18.0 BiocGenerics_0.4.0 gplots_2.11.0 MASS_7.3-23 KernSmooth_2.23-10 caTools_1.14 gdata_2.12.0.2 gtools_2.7.1 stringr_0.6.2 loaded via a namespace (and not attached): [1] annotate_1.36.0 AnnotationDbi_1.20.7 bitops_1.0-5 DBI_0.2-7 genefilter_1.40.0 geneplotter_1.36.0 IRanges_1.16.6 parallel_2.15.1 RColorBrewer_1.0-5 RSQLite_0.11.3 splines_2.15.1 stats4_2.15.1 survival_2.37-4 XML_3.96-1.1 xtable_1.7-1 </pre> <hr/><div class="infomessage">This tool (edgeR) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/> </div></body></html>