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| Output File Name (click to view) | Size |
|---|---|
| edgeR.Rscript | 19.7 KB) |
| edgeR_runner.log | 79.2 KB) |
| edgeRtest_BCV_vs_abundance.pdf | 16.4 KB) |
| edgeRtest_DESeq_TopTable.xls | 135.1 KB) |
| edgeRtest_MDSplot.pdf | 4.9 KB) |
| edgeRtest_RowsumCum.pdf | 6.3 KB) |
| edgeRtest_Smearplot.pdf | 16.7 KB) |
| edgeRtest_VOOM_topTable.xls | 131.4 KB) |
| edgeRtest_heatmap.pdf | 11.3 KB) |
| edgeRtest_pval_qq.pdf | 15.9 KB) |
| edgeRtest_sampleBoxplot.pdf | 7.8 KB) |
| edgeRtest_samplehistplot.pdf | 10.9 KB) |
| edgeRtest_venn.pdf | 9.7 KB) |
| edgeRtest_voomplot.pdf | 16.7 KB) |
Rscript log
## 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
0610005C13Rik 0610007N19Rik 0610008F07Rik 0610009L18Rik 0610012G03Rik 0610031O16Rik# 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 Mir122a
Mir192 490327 630849 526600 2325567 Mir192
Mir208b 0 0 0 14756 Mir208b
Mir208a 0 0 1 4638 Mir208a
Mir499 0 0 0 6527 Mir499
Mir149 9 8 16 6164 Mir149
Mir490 1 0 1 1741 Mir490
Mir802 401 209 352 1514 Mir802
Mir204 2 1 9 2601 Mir204
Mir1948 648 259 617 2404 Mir1948
Mir3073 218 131 214 904 Mir3073
Mir194-2 865 439 880 3570 Mir194-2
Mir10b 1080 1189 1777 197340 Mir10b
Mir101b 11066 16253 10901 59019 Mir101b
Mir182 879 3409 1075 7189 Mir182
Mir200b 164 66 155 888 Mir200b
Mir181c 366 384 427 23605 Mir181c
Mir181d 42 46 38 2139 Mir181d
Mir21 44582 43237 50530 229120 Mir21
Mir199b 1 0 4 370 Mir199b
Mir193 101 61 83 421 Mir193
Mir23a 229 218 327 10118 Mir23a
Mir195 112 75 120 3962 Mir195
Ahsg 18 879 40 1524 Ahsg
Mir148a 177349 256441 193465 1002397 Mir148a
Dnm3os 36 20 40 1401 Dnm3os
Mir27a 628 400 760 21886 Mir27a
Mir429 82 41 101 499 Mir429
Mir214 26 17 29 1048 Mir214
Mir200a 53 33 47 264 Mir200a
Mir194-1 160 81 141 635 Mir194-1
Mir378 90 123 106 4075 Mir378
Mir322 228 91 224 7074 Mir322
Mir215 31 28 36 1182 Mir215
Cyp3a25 30 93 27 226 Cyp3a25
Mir183 71 181 130 563 Mir183
Mir181a-2 69 115 82 2817 Mir181a-2
Mir155 3 8 9 463 Mir155
Snord91a 256 358 285 1437 Snord91a
Mir125b-2 149 60 133 3837 Mir125b-2
Serpina4-ps1 19 117 14 295 Serpina4-ps1
Mir133b 0 0 0 159 Mir133b
Gm10069 12 701 37 1309 Gm10069
Mir871 81 29 93 290 Mir871
Mir184 0 2 2 247 Mir184
Mir132 22 30 28 857 Mir132
Snord104 5610 7452 6017 33458 Snord104
Mir3074-2 127 65 140 3470 Mir3074-2
Mir24-2 127 65 140 3470 Mir24-2
5430416N02Rik 99 79 141 564 5430416N02Rik
[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