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<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_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_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_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_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_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>&nbsp;</td>
</tr></table></div>

<div class="toolFormTitle">DESeq2 log output</div>

<pre>

# DESeq top 50

                     Contig     baseMean log2FoldChange     lfcSE       stat        pvalue          padj  NReads                                                                                               URL

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>

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      -6.947219 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      -3.104596 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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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      -2.173582 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      -2.174835 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>

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>

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>

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      -2.725743 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      -2.725743 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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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      -3.046196 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      -3.049266 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>

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>

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>

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>

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>

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>

<div class="toolFormTitle">DifferentialCounts log output</div>

<pre>

KernSmooth 2.23 loaded

Copyright M. P. Wand 1997-2009

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Loading required package: limma

Loading required package: methods

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 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:limma’:

    plotMA

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    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

Attaching package: ‘IRanges’

The following object is masked from ‘package:gplots’:

    space

Loading required package: GenomeInfoDb

Loading required package: Rcpp

Loading required package: RcppArmadillo

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_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_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>

<div class="toolFormTitle">VOOM log output</div>

<pre>

# VOOM top 50

                   logFC    AveExpr          t      P.Value    adj.P.Val         B  NReads                                                                                               URL

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       -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>

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>

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       -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>

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>

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>

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>

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>

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>

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>

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         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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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>

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         -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>

<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_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_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_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_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_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_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_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>&nbsp;</td><td>&nbsp;</td>
</tr></table></div>

<div class="toolFormTitle">edgeR log output</div>

<pre>

[1] Common Dispersion = 0.228651459675839 CV =  0.478175134940995 getPriorN =  3.33333333333333

[1] "No GLM fit outlier genes found\n"

[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  7.737466e-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  2.740528e-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  3.313429e-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  7.930762e-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  6.710365e-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 217.22866  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 212.88058  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>

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  7.883296e-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  9.778601e-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 147.24792  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  1.703813e-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  2.919521e-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>

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 0.06896653     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>

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  5.031521e-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  5.154209e-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  5.723023e-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  2.997457e-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  4.809370e-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  3.620939e-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  1.851472e-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  5.651423e-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  2.854936e-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  3.100028e-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  5.764005e-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  8.137283e-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>

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_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" 
                           alt="Image called sample_counts_histogram.pdf"/></a></td>

<td>&nbsp;</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 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 =  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 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 3.1.0 (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=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   stats     graphics  grDevices utils     datasets  base     

other attached packages:

 [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_1.42.1      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>

<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>10.5 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>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_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>