DESeq2 images and outputs
(Click on a thumbnail image to download the corresponding original PDF image) |
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DESeq2 log output
# 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 Mir122a
Mir192 Mir192 271352.97636 6.994296 0.2346736 29.804353 3.430828e-195 1.444379e-192 2325567 Mir192
Mir149 Mir149 810.35429 -6.947219 0.2752144 -25.242938 1.353995e-140 3.800212e-138 6164 Mir149
Mir23a Mir23a 1289.18043 -3.104596 0.1650418 -18.810968 6.140634e-79 1.292603e-76 10118 Mir23a
Mir204 Mir204 347.57397 -7.385478 0.4210055 -17.542475 6.790394e-69 1.143502e-66 2601 Mir204
Mir10b Mir10b 27820.40551 -5.122625 0.3095281 -16.549791 1.606588e-61 2.254579e-59 197340 Mir10b
Mir194-2 Mir194-2 391.65678 5.272315 0.3261217 16.166709 8.660202e-59 1.041699e-56 3570 Mir194-2
Mir181d Mir181d 275.22797 -3.578479 0.2232474 -16.029209 7.989327e-58 8.408767e-56 2139 Mir181d
Mir27a Mir27a 2788.72629 -3.022597 0.1992370 -15.170866 5.514410e-52 5.159037e-50 21886 Mir27a
Mir181c Mir181c 2765.96510 -3.678297 0.2459044 -14.958240 1.376168e-50 1.158734e-48 23605 Mir181c
Mir195 Mir195 519.86200 -3.158968 0.2124717 -14.867713 5.340712e-50 4.088073e-48 3962 Mir195
Mir208b Mir208b 1649.77924 -12.247146 0.8586111 -14.263905 3.673137e-46 2.577318e-44 14756 Mir208b
Mir1948 Mir1948 263.89527 7.281854 0.5169425 14.086391 4.604994e-45 2.982619e-43 2404 Mir1948
Mir490 Mir490 220.99790 -8.314250 0.5954353 -13.963315 2.610066e-44 1.569768e-42 1741 Mir490
Mir23b Mir23b 2028.55377 -2.066561 0.1531073 -13.497466 1.618477e-41 9.085049e-40 16387 Mir23b
Mir21 Mir21 26121.31011 2.974199 0.2230949 13.331544 1.517256e-40 7.984558e-39 229120 Mir21
Mir101b Mir101b 6846.19683 3.823085 0.2899493 13.185354 1.065529e-39 5.277502e-38 59019 Mir101b
Mir208a Mir208a 616.76981 -11.025006 0.8475353 -13.008316 1.097341e-38 5.133115e-37 4638 Mir208a
Dnm3os Dnm3os 179.61643 -3.289322 0.2559302 -12.852417 8.336403e-38 3.694343e-36 1401 Dnm3os
Mir215 Mir215 152.78082 -3.012902 0.2351528 -12.812528 1.395132e-37 5.873506e-36 1182 Mir215
Mir214 Mir214 134.69038 -3.229468 0.2571076 -12.560766 3.469589e-36 1.391140e-34 1048 Mir214
Mir203 Mir203 772.92882 1.991755 0.1694325 11.755450 6.620692e-32 2.533919e-30 6739 Mir203
Mir499 Mir499 712.45950 -11.716229 1.0177724 -11.511639 1.152660e-30 4.219739e-29 6527 Mir499
Mir27b Mir27b 76478.05753 -1.906131 0.1672784 -11.394959 4.430372e-30 1.554322e-28 625308 Mir27b
Mir322 Mir322 899.53469 -3.147196 0.2773005 -11.349407 7.466726e-30 2.514793e-28 7074 Mir322
Rabggtb Rabggtb 2257.19195 1.991117 0.1756753 11.334078 8.896442e-30 2.881079e-28 19535 Rabggtb
Mir143hg Mir143hg 180217.77425 -2.173582 0.1966899 -11.050806 2.172555e-28 6.775153e-27 1407364 Mir143hg
Mir143 Mir143 179219.35960 -2.174835 0.1975414 -11.009513 3.438555e-28 1.034023e-26 1399819 Mir143
Mir378 Mir378 483.21548 -3.012592 0.2747646 -10.964266 5.675913e-28 1.647972e-26 4075 Mir378
Mir132 Mir132 106.46062 -2.793901 0.2568175 -10.878935 1.452498e-27 4.076678e-26 857 Mir132
Mir155 Mir155 57.66182 -3.815683 0.3605552 -10.582799 3.580985e-26 9.726416e-25 463 Mir155
Mir24-2 Mir24-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 Mir24-2
Mir3074-2 Mir3074-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 Mir3074-2
Mir125b-2 Mir125b-2 493.08516 -2.938770 0.2803125 -10.483910 1.024200e-25 2.536401e-24 3837 Mir125b-2
Mir150 Mir150 553.20599 -2.856250 0.2760016 -10.348671 4.243363e-25 1.020832e-23 4229 Mir150
Mir182 Mir182 886.79583 5.089394 0.4937848 10.306907 6.557770e-25 1.533789e-23 7189 Mir182
Mir148a Mir148a 118994.46955 2.695116 0.2621094 10.282410 8.458605e-25 1.924904e-23 1002397 Mir148a
Mir199b Mir199b 47.84725 -5.417036 0.5304738 -10.211694 1.757697e-24 3.894687e-23 370 Mir199b
Snord104 Snord104 3851.90119 2.396960 0.2371478 10.107451 5.119918e-24 1.105377e-22 33458 Snord104
Mir193 Mir193 45.70861 5.113887 0.5386870 9.493243 2.239557e-21 4.714267e-20 421 Mir193
Mir200b Mir200b 87.13638 6.279428 0.6679043 9.401688 5.369454e-21 1.102703e-19 888 Mir200b
5430416N02Rik 5430416N02Rik 62.15966 3.116558 0.3399987 9.166382 4.891610e-20 9.806514e-19 564 5430416N02Rik
Mir802 Mir802 166.83414 9.771028 1.0750153 9.089199 9.977106e-20 1.953657e-18 1514 Mir802
Mir125b-1 Mir125b-1 79.01988 -3.046196 0.3356809 -9.074680 1.140124e-19 2.181783e-18 609 Mir125b-1
2610203C20Rik 2610203C20Rik 79.17666 -3.049266 0.3363186 -9.066600 1.227890e-19 2.297519e-18 610 2610203C20Rik
Snord91a Snord91a 168.95251 2.722976 0.3035329 8.970941 2.939927e-19 5.381346e-18 1437 Snord91a
Mir194-1 Mir194-1 71.10636 3.788463 0.4230333 8.955471 3.382877e-19 6.060389e-18 635 Mir194-1
Mir181a-1 Mir181a-1 59.53826 -3.173584 0.3580582 -8.863320 7.766622e-19 1.362395e-17 506 Mir181a-1
Mir181a-2 Mir181a-2 347.82506 -2.863247 0.3233431 -8.855136 8.358205e-19 1.436247e-17 2817 Mir181a-2
Mir184 Mir184 32.23796 -4.996780 0.5668564 -8.814896 1.197967e-18 2.017377e-17 247 Mir184
DifferentialCounts log output
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
VOOM images and outputs
(Click on a thumbnail image to download the corresponding original PDF image) |
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VOOM log output
# 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 Mir192
Mir208a -10.458438 3.8918506 -29.183545 2.249812e-13 1.283518e-10 19.141041 4638 Mir208a
Mir3073 8.318578 2.6485638 25.821264 1.102217e-12 4.192097e-10 18.063600 904 Mir3073
Mir802 8.992449 2.9857711 25.195575 1.514327e-12 4.319618e-10 17.906674 1514 Mir802
Mir208b -12.256447 4.4678897 -22.360114 7.074494e-12 1.614400e-09 16.920424 14756 Mir208b
Mir499 -11.104485 3.8066799 -21.990054 8.769804e-12 1.667724e-09 16.728874 6527 Mir499
Mir10b -4.775768 12.4173688 -21.487387 1.180685e-11 1.924516e-09 17.249348 197340 Mir10b
Mir148a 2.751538 15.4237642 20.289553 2.464883e-11 3.515539e-09 16.455471 1002397 Mir148a
Mir490 -8.497742 3.6613221 -18.336110 8.980482e-11 1.138526e-08 13.923237 1741 Mir490
Mir122a 10.197963 8.1512374 17.467826 1.663427e-10 1.897970e-08 14.215445 90428 Mir122a
Mir133b -6.172367 1.3497975 -17.274094 1.916064e-10 1.987481e-08 13.840201 159 Mir133b
Mir149 -7.041176 6.0886889 -16.861286 2.602547e-10 2.474589e-08 13.714880 6164 Mir149
Mir101b 3.837883 10.6216725 15.443054 7.873164e-10 6.910215e-08 13.054350 59019 Mir101b
Mir143 -1.912927 16.0353646 -14.922755 1.209475e-09 9.857220e-08 12.374988 1399819 Mir143
Mir194-2 5.534694 6.2627211 14.703097 1.455682e-09 1.107289e-07 12.316769 3570 Mir194-2
Mir23a -2.905961 8.6431895 -14.558394 1.646894e-09 1.174441e-07 12.339306 10118 Mir23a
Mir1983 -5.612359 1.1061384 -14.266537 2.119488e-09 1.422551e-07 11.743589 101 Mir1983
Mir27a -2.849084 10.0939084 -14.158498 2.329669e-09 1.476752e-07 11.960195 21886 Mir27a
Cyp3a25 6.312461 1.6425308 13.845627 3.074630e-09 1.846396e-07 11.502713 226 Cyp3a25
Mir200a 6.129125 1.8320913 13.226966 5.410979e-09 3.086963e-07 10.979834 264 Mir200a
Mir181d -3.405544 6.3702152 -13.064584 6.300369e-09 3.423201e-07 11.006301 2139 Mir181d
Mir153 -5.698257 1.5328802 -12.832092 7.856705e-09 3.829623e-07 10.583835 140 Mir153
Mir204 -7.718081 4.5031856 -12.808496 8.036265e-09 3.829623e-07 10.353229 2601 Mir204
Gm5441 -5.716851 1.5430406 -12.806028 8.055298e-09 3.829623e-07 10.562881 142 Gm5441
Rabggtb 2.327908 9.9369857 12.760291 8.416902e-09 3.841474e-07 10.654006 19535 Rabggtb
Mir504 -5.122304 0.8161671 -12.391521 1.205304e-08 5.289430e-07 10.144865 69 Mir504
Mir133a-1 -4.912497 0.7297882 -12.335045 1.274466e-08 5.385801e-07 10.076395 60 Mir133a-1
Mir195 -2.954216 7.3530970 -12.081859 1.641098e-08 6.603731e-07 10.055879 3962 Mir195
Mir27b -1.496991 14.9464877 -12.059553 1.678424e-08 6.603731e-07 9.674850 625308 Mir27b
Snord52 2.631712 9.7652181 11.922618 1.928407e-08 7.334374e-07 9.811774 18059 Snord52
Mir322 -3.029558 8.1188344 -11.736839 2.333148e-08 8.587488e-07 9.679815 7074 Mir322
Mir181c -3.676262 9.6244506 -11.575598 2.758358e-08 9.835271e-07 9.453057 23605 Mir181c
Mir1948 7.101780 4.7821564 11.471202 3.077353e-08 1.033009e-06 9.233632 2404 Mir1948
0610031O16Rik 4.519875 0.7388871 11.470939 3.078205e-08 1.033009e-06 9.284014 78 0610031O16Rik
Mir201 -4.964105 0.7490919 -11.289794 3.729283e-08 1.210650e-06 9.114028 63 Mir201
Mir21 2.746616 13.2835800 11.267331 3.819755e-08 1.210650e-06 8.925217 229120 Mir21
Mir184 -5.569565 2.3521173 -11.190343 4.148052e-08 1.279170e-06 8.854599 247 Mir184
1810019D21Rik 5.164581 1.0784751 11.082009 4.662057e-08 1.399844e-06 8.951908 117 1810019D21Rik
Mir203 2.216791 8.5426169 10.866758 5.896538e-08 1.725115e-06 8.715639 6739 Mir203
1110038B12Rik 2.383720 10.6847245 10.832157 6.125623e-08 1.744094e-06 8.573067 37066 1110038B12Rik
Snord104 2.571210 10.4798167 10.811468 6.267120e-08 1.744094e-06 8.561110 33458 Snord104
Mir182 5.196800 7.2088299 10.640454 7.579543e-08 2.021320e-06 8.545839 7189 Mir182
Mir547 -4.542934 0.5799793 -10.635980 7.617593e-08 2.021320e-06 8.435473 42 Mir547
Mir143hg -2.291921 16.3789153 -10.597275 7.955395e-08 2.062978e-06 7.952584 1407364 Mir143hg
Scnn1b -4.541403 0.5700621 -10.243065 1.190487e-07 3.018546e-06 8.023327 45 Scnn1b
Mir125b-2 -2.896115 7.2737925 -10.091091 1.420082e-07 3.522420e-06 7.876068 3837 Mir125b-2
Mir1a-1 -4.402568 0.4498447 -9.950346 1.675164e-07 4.066729e-06 7.692790 42 Mir1a-1
Mir378 -2.733247 7.2964165 -9.922980 1.730212e-07 4.112858e-06 7.672216 4075 Mir378
Mir199b -5.651345 2.8029895 -9.883978 1.812024e-07 4.219426e-06 7.548022 370 Mir199b
Mir155 -4.158272 3.8002361 -9.845490 1.896814e-07 4.328530e-06 7.604112 463 Mir155
edgeR images and outputs
(Click on a thumbnail image to download the corresponding original PDF image) |
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edgeR log output
[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 Mir208a
Mir149 Mir149 -7.008984 8.861767 484.30321 2.473909e-107 1.411365e-104 0.04959937 6164 Mir149
Mir208b Mir208b -13.291635 9.905945 417.69758 7.737466e-93 2.942816e-90 0.10508096 14756 Mir208b
Mir122a Mir122a 10.514683 12.478088 415.17429 2.740528e-92 7.817355e-90 0.10803882 90428 Mir122a
Mir204 Mir204 -7.498162 7.634507 341.30678 3.313429e-76 7.561245e-74 0.06907958 2601 Mir204
Mir499 Mir499 -13.577454 8.700078 325.79199 7.930762e-73 1.508166e-70 0.12042284 6527 Mir499
Mir490 Mir490 -8.534394 6.991023 303.17184 6.710365e-68 1.093790e-65 0.07949711 1741 Mir490
Mir192 Mir192 6.953853 17.169364 217.22866 3.638312e-49 5.189142e-47 0.12700995 2325567 Mir192
Mir802 Mir802 11.440805 6.593380 212.88058 3.231647e-48 4.097010e-46 0.12273671 1514 Mir802
Mir1948 Mir1948 7.418142 7.252734 195.66958 1.840248e-44 2.099723e-42 0.12060221 2404 Mir1948
Mir194-2 Mir194-2 5.298950 7.811522 191.85588 1.250960e-43 1.297587e-41 0.08670751 3570 Mir194-2
Mir23a Mir23a -3.153807 9.529402 177.53185 1.676248e-40 1.593833e-38 0.04442763 10118 Mir23a
Mir181c Mir181c -3.767686 10.639598 169.87390 7.883296e-39 6.919108e-37 0.06368883 23605 Mir181c
Mir3073 Mir3073 10.686337 5.859950 164.86740 9.778601e-38 7.969560e-36 0.14069249 904 Mir3073
Mir181d Mir181d -3.643963 7.300371 162.18591 3.767663e-37 2.865936e-35 0.05729574 2139 Mir181d
Mir195 Mir195 -3.203683 8.215089 150.20548 1.563314e-34 1.114838e-32 0.05235020 3962 Mir195
Mir10b Mir10b -5.182616 13.946466 147.24792 6.926822e-34 4.649120e-32 0.12268790 197340 Mir10b
Mir101b Mir101b 3.759962 11.863187 136.31359 1.703813e-31 1.080028e-29 0.07961343 59019 Mir101b
Mir378 Mir378 -3.115599 8.119617 126.76408 2.092233e-29 1.256441e-27 0.05942391 4075 Mir378
Mir27a Mir27a -3.064687 10.642480 124.98911 5.117477e-29 2.919521e-27 0.06113852 21886 Mir27a
Mir182 Mir182 5.057509 8.846381 123.17765 1.275060e-28 6.927826e-27 0.13653707 7189 Mir182
Mir322 Mir322 -3.194159 9.012888 107.34926 3.732413e-25 1.935765e-23 0.07536483 7074 Mir322
Mir199b Mir199b -5.520119 4.792610 102.10724 5.259607e-24 2.609223e-22 0.13417024 370 Mir199b
Mir181a-2 Mir181a-2 -3.000177 7.637692 101.38361 7.578821e-24 3.603098e-22 0.06896653 2817 Mir181a-2
Mir125b-2 Mir125b-2 -2.987759 8.144514 91.72544 9.957640e-22 4.488356e-20 0.07737381 3837 Mir125b-2
Dnm3os Dnm3os -3.331215 6.686950 91.67250 1.022763e-21 4.488356e-20 0.08810497 1401 Dnm3os
Mir184 Mir184 -5.111350 4.234160 84.35542 4.133639e-20 1.686711e-18 0.13502324 247 Mir184
Mir215 Mir215 -3.058208 6.447966 84.35278 4.139167e-20 1.686711e-18 0.08138517 1182 Mir215
Mir133b Mir133b -8.383611 3.584760 83.96681 5.031521e-20 1.960318e-18 0.17482280 159 Mir133b
Mir150 Mir150 -2.883446 8.307765 83.91918 5.154209e-20 1.960318e-18 0.08008123 4229 Mir150
Mir3074-2 Mir3074-2 -2.778308 7.935651 83.74839 5.619282e-20 2.040616e-18 0.07424646 3470 Mir3074-2
Mir24-2 Mir24-2 -2.778307 7.935651 83.71222 5.723023e-20 2.040616e-18 0.07427992 3470 Mir24-2
Mir193 Mir193 5.176579 4.801090 83.19222 7.445011e-20 2.574169e-18 0.14794861 421 Mir193
Scarna17 Scarna17 2.182159 9.244479 81.91330 1.421894e-19 4.771710e-18 0.04982909 9224 Scarna17
Mir214 Mir214 -3.271172 6.271755 80.43948 2.997457e-19 9.771711e-18 0.09566584 1048 Mir214
Snord104 Snord104 2.330488 11.053611 79.50529 4.809370e-19 1.524303e-17 0.05915990 33458 Snord104
Mir200a Mir200a 7.201555 4.139422 77.35503 1.428304e-18 4.365755e-17 0.19287764 264 Mir200a
Mir200b Mir200b 6.525423 5.752604 77.31985 1.453976e-18 4.365755e-17 0.26237966 888 Mir200b
Mir21 Mir21 2.923147 13.825255 75.51798 3.620939e-18 1.059357e-16 0.09395834 229120 Mir21
Mir203 Mir203 1.956427 8.767610 75.17870 4.299815e-18 1.226522e-16 0.04381710 6739 Mir203
Mir155 Mir155 -3.886731 5.068563 73.81316 8.587210e-18 2.389758e-16 0.12522673 463 Mir155
Cyp3a25 Cyp3a25 8.681501 3.972085 72.29680 1.851472e-17 5.029834e-16 0.23125383 226 Cyp3a25
Rabggtb Rabggtb 1.934093 10.298211 72.02043 2.129809e-17 5.651423e-16 0.04596646 19535 Rabggtb
Mir23b Mir23b -2.100584 10.184110 71.44225 2.854936e-17 7.403367e-16 0.05416378 16387 Mir23b
Snord52 Snord52 2.207491 10.217554 71.27974 3.100028e-17 7.860292e-16 0.05941483 18059 Snord52
Gm5441 Gm5441 -6.881248 3.538457 70.05615 5.764005e-17 1.429724e-15 0.20097284 142 Gm5441
Mir153 Mir153 -6.857671 3.517446 69.37600 8.137283e-17 1.975455e-15 0.20158808 140 Mir153
Mir132 Mir132 -2.858294 5.938312 64.52507 9.531204e-16 2.265647e-14 0.09274248 857 Mir132
1110038B12Rik 1110038B12Rik 2.195962 11.253090 62.92015 2.152583e-15 5.012443e-14 0.06712174 37066 1110038B12Rik
Snord91a Snord91a 2.654072 6.557504 62.40549 2.795431e-15 6.379174e-14 0.08637410 1437 Snord91a
[1] # 416 tags significant at adj p= 0.05
Other images and outputs
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Other log output
## 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] 0610005C13Rik 0610007N19Rik 0610008F07Rik 0610009L18Rik 0610012G03Rik
[6] 0610031O16Rik
[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
All output files available for downloading