# HG changeset patch # User iuc # Date 1424277434 18000 # Node ID e7894f37320af8931bf81055999cbb40da41b0f5 # Parent 9809bcb27cc13d5d071b07cb959180bb782a27c2 Uploaded diff -r 9809bcb27cc1 -r e7894f37320a rgedgeRpaired_nocamera.xml --- a/rgedgeRpaired_nocamera.xml Wed Jan 07 05:45:33 2015 -0500 +++ b/rgedgeRpaired_nocamera.xml Wed Feb 18 11:37:14 2015 -0500 @@ -131,7 +131,7 @@ - + @@ -1063,6 +1063,9 @@ .. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html .. _Galaxy: http://getgalaxy.org + + doi: 10.1093/bioinformatics/btp616 + diff -r 9809bcb27cc1 -r e7894f37320a test-data/edgeRtest1out.html --- a/test-data/edgeRtest1out.html Wed Jan 07 05:45:33 2015 -0500 +++ b/test-data/edgeRtest1out.html Wed Feb 18 11:37:14 2015 -0500 @@ -8,7 +8,7 @@
-
Galaxy Tool "Differential_Counts" run at 28/12/2014 21:02:37

+
Galaxy Tool "Differential_Counts" run at 18/02/2015 14:14:12

DESeq2 images and outputs
(Click on a thumbnail image to download the corresponding original PDF image)
@@ -40,105 +40,105 @@ Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL -Mir192 Mir192 271352.97636 6.965264 0.2150593 32.387646 4.096935e-230 3.818343e-227 2325567 Mir192 +Mir122a Mir122a 10112.31117 10.433687 0.3440661 30.324653 5.425198e-202 4.568017e-199 90428 Mir122a -Mir122a Mir122a 10112.31117 10.312083 0.3292695 31.318061 2.649329e-215 1.234587e-212 90428 Mir122a +Mir192 Mir192 271352.97636 6.994296 0.2346736 29.804353 3.430828e-195 1.444379e-192 2325567 Mir192 -Mir149 Mir149 810.35429 -6.911118 0.2341392 -29.517132 1.735536e-191 5.391733e-189 6164 Mir149 +Mir149 Mir149 810.35429 -6.947219 0.2752144 -25.242938 1.353995e-140 3.800212e-138 6164 Mir149 -Mir23a Mir23a 1289.18043 -3.104086 0.1191688 -26.047815 1.424245e-149 3.318491e-147 10118 Mir23a +Mir23a Mir23a 1289.18043 -3.104596 0.1650418 -18.810968 6.140634e-79 1.292603e-76 10118 Mir23a -Mir181d Mir181d 275.22797 -3.581172 0.1778187 -20.139461 3.329373e-90 6.205952e-88 2139 Mir181d +Mir204 Mir204 347.57397 -7.385478 0.4210055 -17.542475 6.790394e-69 1.143502e-66 2601 Mir204 -Mir204 Mir204 347.57397 -7.284200 0.3771119 -19.315751 3.959346e-83 6.150183e-81 2601 Mir204 +Mir10b Mir10b 27820.40551 -5.122625 0.3095281 -16.549791 1.606588e-61 2.254579e-59 197340 Mir10b -Mir23b Mir23b 2028.55377 -2.065110 0.1085802 -19.019217 1.182361e-80 1.574229e-78 16387 Mir23b +Mir194-2 Mir194-2 391.65678 5.272315 0.3261217 16.166709 8.660202e-59 1.041699e-56 3570 Mir194-2 -Mir27a Mir27a 2788.72629 -3.016676 0.1688167 -17.869539 2.036708e-71 2.372765e-69 21886 Mir27a +Mir181d Mir181d 275.22797 -3.578479 0.2232474 -16.029209 7.989327e-58 8.408767e-56 2139 Mir181d -Mir195 Mir195 519.86200 -3.152795 0.1784796 -17.664734 7.838131e-70 8.116820e-68 3962 Mir195 +Mir27a Mir27a 2788.72629 -3.022597 0.1992370 -15.170866 5.514410e-52 5.159037e-50 21886 Mir27a -Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 16.852045 1.013492e-63 9.445744e-62 3570 Mir194-2 +Mir181c Mir181c 2765.96510 -3.678297 0.2459044 -14.958240 1.376168e-50 1.158734e-48 23605 Mir181c -Mir208b Mir208b 1649.77924 -11.396172 0.6771238 -16.830264 1.464482e-63 1.240816e-61 14756 Mir208b +Mir195 Mir195 519.86200 -3.158968 0.2124717 -14.867713 5.340712e-50 4.088073e-48 3962 Mir195 -Mir10b Mir10b 27820.40551 -5.071453 0.3044884 -16.655656 2.753110e-62 2.138249e-60 197340 Mir10b +Mir208b Mir208b 1649.77924 -12.247146 0.8586111 -14.263905 3.673137e-46 2.577318e-44 14756 Mir208b -Mir181c Mir181c 2765.96510 -3.660964 0.2275711 -16.087120 3.141152e-58 2.251965e-56 23605 Mir181c +Mir1948 Mir1948 263.89527 7.281854 0.5169425 14.086391 4.604994e-45 2.982619e-43 2404 Mir1948 -Mir208a Mir208a 616.76981 -10.356524 0.6559218 -15.789267 3.688391e-56 2.455415e-54 4638 Mir208a +Mir490 Mir490 220.99790 -8.314250 0.5954353 -13.963315 2.610066e-44 1.569768e-42 1741 Mir490 -Mir490 Mir490 220.99790 -8.059660 0.5142876 -15.671504 2.369067e-55 1.471980e-53 1741 Mir490 +Mir23b Mir23b 2028.55377 -2.066561 0.1531073 -13.497466 1.618477e-41 9.085049e-40 16387 Mir23b -Mir203 Mir203 772.92882 1.990849 0.1274099 15.625546 4.877239e-55 2.840992e-53 6739 Mir203 +Mir21 Mir21 26121.31011 2.974199 0.2230949 13.331544 1.517256e-40 7.984558e-39 229120 Mir21 -Mir215 Mir215 152.78082 -3.004380 0.1939090 -15.493765 3.822341e-54 2.095542e-52 1182 Mir215 +Mir101b Mir101b 6846.19683 3.823085 0.2899493 13.185354 1.065529e-39 5.277502e-38 59019 Mir101b -Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 -15.132265 9.922045e-52 5.137415e-50 1401 Dnm3os +Mir208a Mir208a 616.76981 -11.025006 0.8475353 -13.008316 1.097341e-38 5.133115e-37 4638 Mir208a -Mir214 Mir214 134.69038 -3.216444 0.2154916 -14.926074 2.230149e-50 1.093947e-48 1048 Mir214 +Dnm3os Dnm3os 179.61643 -3.289322 0.2559302 -12.852417 8.336403e-38 3.694343e-36 1401 Dnm3os -Mir21 Mir21 26121.31011 2.963903 0.2008617 14.755939 2.817433e-49 1.312924e-47 229120 Mir21 +Mir215 Mir215 152.78082 -3.012902 0.2351528 -12.812528 1.395132e-37 5.873506e-36 1182 Mir215 -Mir1948 Mir1948 263.89527 7.074045 0.4867226 14.534039 7.374076e-48 3.272685e-46 2404 Mir1948 +Mir214 Mir214 134.69038 -3.229468 0.2571076 -12.560766 3.469589e-36 1.391140e-34 1048 Mir214 -Mir27b Mir27b 76478.05753 -1.904653 0.1312889 -14.507339 1.088626e-47 4.611815e-46 625308 Mir27b +Mir203 Mir203 772.92882 1.991755 0.1694325 11.755450 6.620692e-32 2.533919e-30 6739 Mir203 -Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 14.184987 1.134862e-45 4.598659e-44 19535 Rabggtb +Mir499 Mir499 712.45950 -11.716229 1.0177724 -11.511639 1.152660e-30 4.219739e-29 6527 Mir499 -Mir499 Mir499 712.45950 -10.577061 0.7528467 -14.049423 7.766426e-45 3.015962e-43 6527 Mir499 +Mir27b Mir27b 76478.05753 -1.906131 0.1672784 -11.394959 4.430372e-30 1.554322e-28 625308 Mir27b -Mir101b Mir101b 6846.19683 3.791681 0.2809666 13.495132 1.670548e-41 6.227801e-40 59019 Mir101b +Mir322 Mir322 899.53469 -3.147196 0.2773005 -11.349407 7.466726e-30 2.514793e-28 7074 Mir322 -Mir132 Mir132 106.46062 -2.797928 0.2083376 -13.429779 4.046171e-41 1.450397e-39 857 Mir132 +Rabggtb Rabggtb 2257.19195 1.991117 0.1756753 11.334078 8.896442e-30 2.881079e-28 19535 Rabggtb -Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 -12.868566 6.764677e-38 2.335066e-36 1407364 Mir143hg +Mir143hg Mir143hg 180217.77425 -2.173582 0.1966899 -11.050806 2.172555e-28 6.775153e-27 1407364 Mir143hg -Mir143 Mir143 179219.35960 -2.170303 0.1696199 -12.795094 1.746402e-37 5.813025e-36 1399819 Mir143 +Mir143 Mir143 179219.35960 -2.174835 0.1975414 -11.009513 3.438555e-28 1.034023e-26 1399819 Mir143 -Mir155 Mir155 57.66182 -3.788079 0.3056585 -12.393175 2.845516e-35 9.144898e-34 463 Mir155 +Mir378 Mir378 483.21548 -3.012592 0.2747646 -10.964266 5.675913e-28 1.647972e-26 4075 Mir378 -Mir322 Mir322 899.53469 -3.126011 0.2622596 -11.919531 9.363380e-33 2.908890e-31 7074 Mir322 +Mir132 Mir132 106.46062 -2.793901 0.2568175 -10.878935 1.452498e-27 4.076678e-26 857 Mir132 -Mir378 Mir378 483.21548 -2.994300 0.2577321 -11.617876 3.343461e-31 1.005195e-29 4075 Mir378 +Mir155 Mir155 57.66182 -3.815683 0.3605552 -10.582799 3.580985e-26 9.726416e-25 463 Mir155 -Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 Mir24-2 +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 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 Mir3074-2 +Mir3074-2 Mir3074-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 Mir3074-2 -Mir199b Mir199b 47.84725 -5.294373 0.4644474 -11.399295 4.215163e-30 1.155451e-28 370 Mir199b +Mir125b-2 Mir125b-2 493.08516 -2.938770 0.2803125 -10.483910 1.024200e-25 2.536401e-24 3837 Mir125b-2 -Mir802 Mir802 166.83414 8.816580 0.7782636 11.328527 9.478530e-30 2.523997e-28 1514 Mir802 +Mir150 Mir150 553.20599 -2.856250 0.2760016 -10.348671 4.243363e-25 1.020832e-23 4229 Mir150 -Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 -11.095122 1.324798e-28 3.429754e-27 3837 Mir125b-2 +Mir182 Mir182 886.79583 5.089394 0.4937848 10.306907 6.557770e-25 1.533789e-23 7189 Mir182 -Mir301 Mir301 260.53406 -1.676984 0.1526772 -10.983852 4.570133e-28 1.151179e-26 2119 Mir301 +Mir148a Mir148a 118994.46955 2.695116 0.2621094 10.282410 8.458605e-25 1.924904e-23 1002397 Mir148a -Snord104 Snord104 3851.90119 2.386573 0.2173857 10.978522 4.847915e-28 1.189015e-26 33458 Snord104 +Mir199b Mir199b 47.84725 -5.417036 0.5304738 -10.211694 1.757697e-24 3.894687e-23 370 Mir199b -Mir150 Mir150 553.20599 -2.836881 0.2595088 -10.931734 8.127991e-28 1.942381e-26 4229 Mir150 +Snord104 Snord104 3851.90119 2.396960 0.2371478 10.107451 5.119918e-24 1.105377e-22 33458 Snord104 -Mir148a Mir148a 118994.46955 2.678852 0.2481801 10.793984 3.675045e-27 8.562855e-26 1002397 Mir148a +Mir193 Mir193 45.70861 5.113887 0.5386870 9.493243 2.239557e-21 4.714267e-20 421 Mir193 -5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 10.506053 8.101331e-26 1.841571e-24 564 5430416N02Rik +Mir200b Mir200b 87.13638 6.279428 0.6679043 9.401688 5.369454e-21 1.102703e-19 888 Mir200b -Mir193 Mir193 45.70861 4.991530 0.4814098 10.368568 3.446495e-25 7.647936e-24 421 Mir193 +5430416N02Rik 5430416N02Rik 62.15966 3.116558 0.3399987 9.166382 4.891610e-20 9.806514e-19 564 5430416N02Rik -Mir3073 Mir3073 98.93199 8.208709 0.7944742 10.332254 5.036321e-25 1.091593e-23 904 Mir3073 +Mir802 Mir802 166.83414 9.771028 1.0750153 9.089199 9.977106e-20 1.953657e-18 1514 Mir802 -Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 -10.283590 8.355635e-25 1.769875e-23 609 Mir125b-1 +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 -3.023491 0.2948614 -10.253939 1.136165e-24 2.353124e-23 610 2610203C20Rik +2610203C20Rik 2610203C20Rik 79.17666 -3.049266 0.3363186 -9.066600 1.227890e-19 2.297519e-18 610 2610203C20Rik -Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 -9.812740 9.923710e-23 2.010630e-21 506 Mir181a-1 +Snord91a Snord91a 168.95251 2.722976 0.3035329 8.970941 2.939927e-19 5.381346e-18 1437 Snord91a -Mir184 Mir184 32.23796 -4.865023 0.4962776 -9.803028 1.092606e-22 2.166615e-21 247 Mir184 +Mir194-1 Mir194-1 71.10636 3.788463 0.4230333 8.955471 3.382877e-19 6.060389e-18 635 Mir194-1 -Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 -9.651880 4.826276e-22 9.371019e-21 352 Mir199a-2 +Mir181a-1 Mir181a-1 59.53826 -3.173584 0.3580582 -8.863320 7.766622e-19 1.362395e-17 506 Mir181a-1 -Mir182 Mir182 886.79583 4.919630 0.5101689 9.643140 5.255515e-22 9.996204e-21 7189 Mir182 +Mir181a-2 Mir181a-2 347.82506 -2.863247 0.3233431 -8.855136 8.358205e-19 1.436247e-17 2817 Mir181a-2 -Snord91a Snord91a 168.95251 2.700421 0.2835464 9.523738 1.670595e-21 3.113990e-20 1437 Snord91a +Mir184 Mir184 32.23796 -4.996780 0.5668564 -8.814896 1.197967e-18 2.017377e-17 247 Mir184 @@ -221,9 +221,9 @@ lowess -Loading required package: methods +Loading required package: limma -Loading required package: limma +Loading required package: methods Loading required package: splines @@ -251,7 +251,7 @@ The following objects are masked from ‘package:base’: - anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, 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 + 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 @@ -261,7 +261,7 @@ space -Loading required package: XVector +Loading required package: GenomeInfoDb Loading required package: Rcpp @@ -273,14 +273,6 @@ final dispersion estimates -you had estimated gene-wise dispersions, removing these - -you had estimated fitted dispersions, removing these - -you had estimated gene-wise dispersions, removing these - -you had estimated fitted dispersions, removing these - Warning message: closing unused connection 4 (edgeR.log) @@ -446,7 +438,7 @@ 
 
-[1] Common Dispersion = 0.228651460998105 CV =  0.478175136323613 getPriorN =  3.33333333333333
+[1] Common Dispersion = 0.228651459675839 CV =  0.478175134940995 getPriorN =  3.33333333333333
 
 [1] "No GLM fit outlier genes found\n"
 
@@ -458,19 +450,19 @@
 
 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  7.737463e-93  2.942815e-90 0.10508096    14756             Mir208b
+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  2.740525e-92  7.817349e-90 0.10803882    90428             Mir122a
+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  3.313430e-76  7.561247e-74 0.06907958     2601               Mir204
+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  7.930755e-73  1.508165e-70 0.12042284     6527               Mir499
+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  6.710366e-68  1.093790e-65 0.07949711     1741               Mir490
+Mir490               Mir490  -8.534394  6.991023 303.17184  6.710365e-68  1.093790e-65 0.07949711     1741               Mir490
 
-Mir192               Mir192   6.953853 17.169364 217.22867  3.638307e-49  5.189135e-47 0.12700995  2325567               Mir192
+Mir192               Mir192   6.953853 17.169364 217.22866  3.638312e-49  5.189142e-47 0.12700995  2325567               Mir192
 
-Mir802               Mir802  11.440805  6.593380 212.88059  3.231644e-48  4.097007e-46 0.12273671     1514               Mir802
+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
 
@@ -478,21 +470,21 @@
 
 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  7.883295e-39  6.919107e-37 0.06368883    23605             Mir181c
+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  9.778593e-38  7.969554e-36 0.14069249      904             Mir3073
+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 147.24793  6.926819e-34  4.649118e-32 0.12268790   197340               Mir10b
+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  1.703812e-31  1.080028e-29 0.07961343    59019             Mir101b
+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  2.919520e-27 0.06113852    21886               Mir27a
+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
 
@@ -500,7 +492,7 @@
 
 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 0.06896654     2817         Mir181a-2
+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
 
@@ -510,43 +502,43 @@
 
 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  5.031517e-20  1.960318e-18 0.17482280      159             Mir133b
+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  5.154210e-20  1.960318e-18 0.08008123     4229               Mir150
+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  5.723024e-20  2.040616e-18 0.07427992     3470             Mir24-2
+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  2.997458e-19  9.771712e-18 0.09566584     1048               Mir214
+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  4.809369e-19  1.524303e-17 0.05915990    33458           Snord104
+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  3.620938e-18  1.059357e-16 0.09395834   229120                 Mir21
+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  1.851471e-17  5.029829e-16 0.23125383      226             Cyp3a25
+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  5.651422e-16 0.04596646    19535             Rabggtb
+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  2.854935e-17  7.403367e-16 0.05416378    16387               Mir23b
+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  3.100027e-17  7.860292e-16 0.05941483    18059             Snord52
+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  5.764004e-17  1.429724e-15 0.20097284      142               Gm5441
+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  8.137282e-17  1.975455e-15 0.20158808      140               Mir153
+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
 
@@ -567,9 +559,9 @@
 
 Got TCols=1 5 6 7; CCols=2 3 4 8
 
-R version 3.0.2 (2013-09-25)
+R version 3.1.0 (2014-04-10)
 
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-unknown-linux-gnu (64-bit)
 
 locale:
 
@@ -581,11 +573,11 @@
 
 other attached packages:
 
- [1] RColorBrewer_1.0-5      DESeq2_1.2.10           RcppArmadillo_0.4.400.0 Rcpp_0.11.2             GenomicRanges_1.14.4    XVector_0.2.0           IRanges_1.20.7          BiocGenerics_0.8.0      edgeR_3.4.2             limma_3.18.13           gplots_2.15.0           stringr_0.6.2          
+ [1] RColorBrewer_1.1-2        DESeq2_1.4.5              RcppArmadillo_0.4.600.4.0 Rcpp_0.11.4               GenomicRanges_1.16.4      GenomeInfoDb_1.0.2        IRanges_1.22.10           BiocGenerics_0.10.0       stringr_0.6.2             edgeR_3.6.8               limma_3.20.9              gplots_2.16.0            
 
 loaded via a namespace (and not attached):
 
- [1] annotate_1.40.1      AnnotationDbi_1.24.0 Biobase_2.22.0       bitops_1.0-6         caTools_1.17.1       DBI_0.3.0            gdata_2.13.3         genefilter_1.44.0    grid_3.0.2           gtools_3.4.1         KernSmooth_2.23-13   lattice_0.20-29      locfit_1.5-9.1       RSQLite_0.11.4       stats4_3.0.2         survival_2.37-7      XML_3.98-1.1         xtable_1.7-4        
+ [1] annotate_1.42.1      AnnotationDbi_1.26.1 Biobase_2.24.0       bitops_1.0-6         caTools_1.17.1       DBI_0.3.1            gdata_2.13.3         genefilter_1.46.1    geneplotter_1.42.0   grid_3.1.0           gtools_3.4.1         KernSmooth_2.23-13   lattice_0.20-29      locfit_1.5-9.1       RSQLite_1.0.0        stats4_3.1.0         survival_2.37-7      XML_3.98-1.1         xtable_1.7-4         XVector_0.4.0
@@ -595,15 +587,15 @@
- + - - - + + + - - + + @@ -614,7 +606,7 @@ - +
Output File Name (click to view)Size
DESeq2.log10.5 KB
DESeq2_edgeRtest_MA_plot.pdf15.0 KB
DESeq2_edgeRtest_MA_plot.pdf14.9 KB
DESeq2_edgeRtest_PCA_plot.pdf4.9 KB
DESeq2_edgeRtest_dispersion_estimates.pdf190.6 KB
DESeq2_edgeRtest_qqplot.pdf13.3 KB
DESeq2_edgeRtest_sample_distance_plot.pdf9.5 KB
DESeq2_edgeRtest_dispersion_estimates.pdf188.4 KB
DESeq2_edgeRtest_qqplot.pdf12.8 KB
DESeq2_edgeRtest_sample_distance_plot.pdf9.4 KB
Differential.log1.4 KB
Differential_Counts.Rscript28.3 KB
Differential_Counts_error.log1.8 KB
Differential_Counts_runner.log1.3 KB
Differential_Counts_error.log1.6 KB
Differential_Counts_runner.log1.4 KB
Differential_rowsum_bar_charts.pdf6.3 KB
Differential_venn_edgeRtest_significant_genes_overlap.pdf9.7 KB
VOOM.log10.1 KB
edgeR_edgeRtest_GoodnessofFit.pdf13.1 KB
edgeR_edgeRtest_MDSplot.pdf4.9 KB
edgeR_edgeRtest_qqplot.pdf15.2 KB
edgeR_edgeRtest_smearplot.pdf16.7 KB
edgeR_edgeRtest_smearplot.pdf16.6 KB
edgeR_edgeRtest_top_100_heatmap.pdf11.2 KB

diff -r 9809bcb27cc1 -r e7894f37320a test-data/edgeRtest1out.xls --- a/test-data/edgeRtest1out.xls Wed Jan 07 05:45:33 2015 -0500 +++ b/test-data/edgeRtest1out.xls Wed Feb 18 11:37:14 2015 -0500 @@ -1,1142 +1,1142 @@ Name logFC logCPM LR PValue adj.p.value Dispersion totreads 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 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 -Mir208a -11.840750632598 8.46501715136261 594.169461743406 3.10454347546078e-131 3.54228410550075e-128 0.0517121951967719 4638 0 0 0 0.539638866040004 789.596577514809 739.374891373071 627.962821069374 673.126883915814 0 0 0 1 1060 956 1693 928 -Mir149 -7.00898388335376 8.86176664758882 484.303208152322 2.47390942925463e-107 1.41136532938977e-104 0.0495993679583824 6164 9.41025046314352 5.51321148265855 4.26049561369029 8.63422185664007 1042.11850183323 868.533475953932 851.254975991856 934.979044577031 25 9 8 16 1399 1123 2295 1289 -Mir208b -13.291634767704 9.90594480087289 417.69757945293 7.73746269808422e-93 2.9428149795047e-90 0.105080963355037 14756 0.376410018525741 0 0 0 1526.30508238476 1273.79753775256 3302.64675652788 1563.13408926571 1 0 0 0 2049 1647 8904 2155 -Mir122a 10.5146833711912 12.4780878408673 415.174288147205 2.74052534761176e-92 7.81734855406255e-90 0.108038824165009 90428 11204.5970214557 14844.628206585 6343.34540683313 13201.1855799366 8.93882917941294 5.41383288662291 10.0147644234336 5.8028179647915 29767 24233 11911 24463 12 7 27 8 -Mir204 -7.49816212335945 7.63450677628189 341.306784530615 3.31342972702995e-76 7.56124663708234e-74 0.0690795844187195 2601 1.8820500926287 1.22515810725746 0.532561951711286 4.85674979436004 425.339288453732 424.599179250854 342.356576401082 392.415564869025 5 2 1 9 571 549 923 541 -Mir499 -13.5774541855867 8.70007828481468 325.791992848402 7.93075479822316e-73 1.50816520412877e-70 0.120422839295321 6527 0 0 0 0 647.32021307582 564.58542960496 1538.19363199923 566.50010381277 0 0 0 0 869 730 4147 781 -Mir490 -8.53439419162448 6.99102321339932 303.171839764489 6.71036610165275e-68 1.0937896745694e-65 0.0794971090139375 1741 1.12923005557722 0.612579053628728 0 0.539638866040004 262.950558361064 240.528861105675 278.187900650933 233.563423082858 3 1 0 1 353 311 750 322 -Mir192 6.95385326892851 17.1693636192881 217.228665712558 3.63830691057425e-49 5.18913523120652e-47 0.127009948729763 2325567 249233.494796504 300364.049628613 335966.174675113 284173.826856666 2394.11641521943 2446.27906005547 2236.25980403264 2358.84550268775 662133 490327 630849 526600 3214 3163 6029 3252 -Mir802 11.4408053854897 6.59338011170441 212.880585690967 3.23164416041045e-48 4.09700665225369e-46 0.122736709286819 1514 207.778330226209 245.64420050512 111.305447907659 189.952880846082 0 0 0 0 552 401 209 352 0 0 0 0 -Mir1948 7.41814210388816 7.25273383973858 195.669583337086 1.84024810781419e-44 2.09972309101599e-42 0.120602206144644 2404 327.100306098869 396.951226751416 137.933545493223 332.957180346683 1.48980486323549 1.54680939617797 1.11275160260373 2.90140898239575 869 648 259 617 2 2 3 4 -Mir194-2 5.29895000039034 7.81152218291727 191.855876444429 1.25095991572432e-43 1.29758660349223e-41 0.0867075108859984 3570 495.355584379875 529.88088138885 233.794696801255 474.882202115204 14.1531462007372 11.6010704713348 7.41834401735823 11.605635929583 1316 865 439 880 19 15 20 16 -Mir23a -3.15380742697919 9.52940174927932 177.53184729458 1.67624826691168e-40 1.59383272712185e-38 0.0444276305475171 10118 163.738358058697 140.280603280979 116.09850547306 176.461909195081 1440.64130274872 1245.95496862136 1320.83615229063 1307.81009881488 435 229 218 327 1934 1611 3561 1803 -Mir181c -3.76768628525284 10.6395980992134 169.873901320388 7.8832945793684e-39 6.91910701158412e-37 0.0636888300973426 23605 213.424480504095 224.203933628114 204.503789457134 230.425795799082 2598.21968148269 2407.60882515102 4385.72498306218 2492.31031587795 567 366 384 427 3488 3113 11824 3436 -Mir3073 10.6863366383691 5.85995006147614 164.867399244026 9.77859349987842e-38 7.96955370240091e-36 0.140692489163711 904 128.355816317278 133.542233691063 69.7656156741785 115.482717332561 0 0 0 0 341 218 131 214 0 0 0 0 -Mir181d -3.64396314910693 7.30037121099239 162.185913876547 3.76766335963997e-37 2.86593592889947e-35 0.057295744087504 2139 22.5846011115444 25.7283202524066 24.4978497787192 20.5062769095202 309.879411552982 262.957597350256 285.97716186916 309.000056625147 60 42 46 38 416 340 771 426 -Mir195 -3.20368283579504 8.21508892700014 150.205483415597 1.563313743885e-34 1.11483811360799e-32 0.0523501994104573 3962 59.472782927067 68.6088540064175 39.9421463783465 64.7566639248005 577.299384503752 535.196051077579 459.195494674474 574.478978514359 158 112 75 120 775 692 1238 792 -Mir10b -5.182615877184 13.9464657676444 147.247925101963 6.92681936835281e-34 4.64911817605327e-32 0.122687897299955 197340 1129.98287561427 661.585377919026 633.216160584719 958.938264953088 25824.277499324 41838.1005478218 19239.4752090186 36019.5418119521 3002 1080 1189 1777 34668 54096 51870 49658 -Mir101b 3.75996221154614 11.8631868690484 136.313586310134 1.70381227672856e-31 1.08002767097072e-29 0.0796134338177996 59019 6422.68414610471 6778.7998074555 8655.72940116353 5882.60327870209 473.013044077268 420.732155760409 735.899726521936 415.626836728191 17063 11066 16253 10901 635 544 1984 573 -Mir378 -3.11559944052724 8.11961743410334 126.764083175197 2.09223329065238e-29 1.25644114980756e-27 0.0594239119916037 4075 51.9445825565522 55.1321148265855 65.5051200604882 57.2017198002405 452.900678423589 436.973654420278 705.113598849899 394.591621605822 138 90 123 106 608 565 1901 544 -Mir27a -3.06468708614932 10.642480146578 124.989109881062 5.11747651268823e-29 2.91952035048864e-27 0.0611385230997705 21886 357.213107580928 384.699645678841 213.024780684514 410.125538190403 2986.31384835554 2774.97605674328 2844.19309625514 2817.26812190627 949 628 400 760 4009 3588 7668 3884 -Mir182 5.0575094804013 8.84638119837792 123.177648902885 1.27505990801811e-28 6.92782550023174e-27 0.136537072604173 7189 622.958580660101 538.456988139652 1815.50369338377 580.111780993005 36.5002191492695 20.1085221503137 20.0295288468672 30.4647943151554 1655 879 3409 1075 49 26 54 42 -Mir322 -3.19415897658088 9.01288823765672 107.349258988254 3.73241270874318e-25 1.93576495485271e-23 0.0753648259256772 7074 98.2430148352183 139.66802422735 48.463137605727 120.879105992961 1012.32240456852 873.947308840555 945.467945012306 893.633966577891 261 228 91 224 1359 1130 2549 1232 -Mir199b -5.5201191226358 4.79261031680931 102.107236112402 5.25960720425951e-24 2.60922253046091e-22 0.134170239329764 370 1.50564007410296 0.612579053628728 0 2.15855546416002 54.3778775080954 49.4979006776952 53.0411597241113 58.753531893514 4 1 0 4 73 64 143 81 -Mir181a-2 -3.0001769666514 7.63769208843994 101.383612144647 7.57882142732892e-24 3.60309802024262e-22 0.0689665350295145 2817 29.3599814450078 42.2679547003822 61.2446244467979 44.2503870152804 353.828655018429 307.815069839417 428.409367002438 322.781749291527 78 69 115 82 475 398 1155 445 -Mir125b-2 -2.98775854400909 8.14451426922916 91.7254418188446 9.95763986706797e-22 4.48835646503007e-20 0.0773738110103449 3837 58.7199628900156 91.2742789906805 31.9537171026772 71.7719691833206 574.319774777281 457.082176570591 476.257685914398 502.669106200064 156 149 60 133 771 591 1284 693 -Dnm3os -3.33121457840666 6.68694995994924 91.6725014252821 1.02276308580878e-21 4.48835646503007e-20 0.0881049738091293 1401 19.9497309818643 22.0528459306342 10.6512390342257 21.5855546416002 180.266388451494 164.735200692954 181.749428425277 222.683139398874 53 36 20 40 242 213 490 307 -Mir184 -5.1113496359546 4.2341598124609 84.355421346379 4.13363865007358e-20 1.68671069592332e-18 0.135023236062136 247 1.50564007410296 0 1.06512390342257 1.07927773208001 40.969633738976 31.7095926216485 33.382548078112 38.4436690167437 4 0 2 2 55 41 90 53 -Mir215 -3.05820800384482 6.4479656700429 84.3527787778146 4.13916735195906e-20 1.68671069592332e-18 0.0813851680057815 1182 21.0789610374415 18.9899506624906 14.911734647916 19.4269991774402 154.194803344873 177.883080560467 145.770459941089 145.795801365386 56 31 28 36 207 230 393 201 -Mir133b -8.38361054384036 3.58476018925042 83.9668081883403 5.03151691897035e-20 1.96031768485074e-18 0.174822803220963 159 0 0 0 0 23.8368778117678 20.1085221503137 28.5606244668292 17.4084538943745 0 0 0 0 32 26 77 24 -Mir150 -2.88344597402096 8.30776498481297 83.9191783201407 5.15420951319212e-20 1.96031768485074e-18 0.0800812276429582 4229 107.653265298362 60.6453263092441 41.5398322334803 91.7386072268007 628.697652285377 529.782218190956 442.504220635418 633.957862653472 286 99 78 170 844 685 1193 874 -Mir3074-2 -2.77830821443436 7.93565101977269 83.7483893415794 5.61928202202066e-20 2.04061561654164e-18 0.0742464608083069 3470 60.97842300117 77.7975398108485 34.6165268612336 75.5494412456006 479.717165961828 357.312970517112 509.64023399251 359.774713817073 162 127 65 140 644 462 1374 496 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