# HG changeset patch # User fubar # Date 1420167187 18000 # Node ID a9ffdf5f7d2a1e7a87d71caeece869b4f2999926 # Parent a95f5496d3306032ec995b5b21ca62eb40dd4cba with tests diff -r a95f5496d330 -r a9ffdf5f7d2a test-data/edgeRtest1out.html --- a/test-data/edgeRtest1out.html Fri Nov 28 06:45:33 2014 -0500 +++ b/test-data/edgeRtest1out.html Thu Jan 01 21:53:07 2015 -0500 @@ -8,26 +8,26 @@

Galaxy Tool "DifferentialCounts" run at 06/10/2014 15:33:02

Galaxy Tool "Differential_Counts" run at 28/12/2014 21:02:37

DESeq2 images and outputs

(Click on a thumbnail image to download the corresponding original PDF image)

- + - + - + - + - +

@@ -40,116 +40,180 @@ 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 6.965264 0.2150593 32.387646 4.096935e-230 3.818343e-227 2325567 Mir192 -Mir192 Mir192 271352.97636 6.994296 0.2346736 29.804353 3.430828e-195 1.444379e-192 2325567 Mir192 +Mir122a Mir122a 10112.31117 10.312083 0.3292695 31.318061 2.649329e-215 1.234587e-212 90428 Mir122a -Mir149 Mir149 810.35429 -6.947219 0.2752144 -25.242938 1.353995e-140 3.800212e-138 6164 Mir149 +Mir149 Mir149 810.35429 -6.911118 0.2341392 -29.517132 1.735536e-191 5.391733e-189 6164 Mir149 -Mir23a Mir23a 1289.18043 -3.104596 0.1650418 -18.810968 6.140634e-79 1.292603e-76 10118 Mir23a +Mir23a Mir23a 1289.18043 -3.104086 0.1191688 -26.047815 1.424245e-149 3.318491e-147 10118 Mir23a -Mir204 Mir204 347.57397 -7.385478 0.4210055 -17.542475 6.790394e-69 1.143502e-66 2601 Mir204 +Mir181d Mir181d 275.22797 -3.581172 0.1778187 -20.139461 3.329373e-90 6.205952e-88 2139 Mir181d -Mir10b Mir10b 27820.40551 -5.122625 0.3095281 -16.549791 1.606588e-61 2.254579e-59 197340 Mir10b +Mir204 Mir204 347.57397 -7.284200 0.3771119 -19.315751 3.959346e-83 6.150183e-81 2601 Mir204 -Mir194-2 Mir194-2 391.65678 5.272315 0.3261217 16.166709 8.660202e-59 1.041699e-56 3570 Mir194-2 +Mir23b Mir23b 2028.55377 -2.065110 0.1085802 -19.019217 1.182361e-80 1.574229e-78 16387 Mir23b -Mir181d Mir181d 275.22797 -3.578479 0.2232474 -16.029209 7.989327e-58 8.408767e-56 2139 Mir181d +Mir27a Mir27a 2788.72629 -3.016676 0.1688167 -17.869539 2.036708e-71 2.372765e-69 21886 Mir27a -Mir27a Mir27a 2788.72629 -3.022597 0.1992370 -15.170866 5.514410e-52 5.159037e-50 21886 Mir27a +Mir195 Mir195 519.86200 -3.152795 0.1784796 -17.664734 7.838131e-70 8.116820e-68 3962 Mir195 -Mir181c Mir181c 2765.96510 -3.678297 0.2459044 -14.958240 1.376168e-50 1.158734e-48 23605 Mir181c +Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 16.852045 1.013492e-63 9.445744e-62 3570 Mir194-2 -Mir195 Mir195 519.86200 -3.158968 0.2124717 -14.867713 5.340712e-50 4.088073e-48 3962 Mir195 +Mir208b Mir208b 1649.77924 -11.396172 0.6771238 -16.830264 1.464482e-63 1.240816e-61 14756 Mir208b -Mir208b Mir208b 1649.77924 -12.247146 0.8586111 -14.263905 3.673137e-46 2.577318e-44 14756 Mir208b +Mir10b Mir10b 27820.40551 -5.071453 0.3044884 -16.655656 2.753110e-62 2.138249e-60 197340 Mir10b -Mir1948 Mir1948 263.89527 7.281854 0.5169425 14.086391 4.604994e-45 2.982619e-43 2404 Mir1948 +Mir181c Mir181c 2765.96510 -3.660964 0.2275711 -16.087120 3.141152e-58 2.251965e-56 23605 Mir181c -Mir490 Mir490 220.99790 -8.314250 0.5954353 -13.963315 2.610066e-44 1.569768e-42 1741 Mir490 +Mir208a Mir208a 616.76981 -10.356524 0.6559218 -15.789267 3.688391e-56 2.455415e-54 4638 Mir208a -Mir23b Mir23b 2028.55377 -2.066561 0.1531073 -13.497466 1.618477e-41 9.085049e-40 16387 Mir23b +Mir490 Mir490 220.99790 -8.059660 0.5142876 -15.671504 2.369067e-55 1.471980e-53 1741 Mir490 -Mir21 Mir21 26121.31011 2.974199 0.2230949 13.331544 1.517256e-40 7.984558e-39 229120 Mir21 +Mir203 Mir203 772.92882 1.990849 0.1274099 15.625546 4.877239e-55 2.840992e-53 6739 Mir203 -Mir101b Mir101b 6846.19683 3.823085 0.2899493 13.185354 1.065529e-39 5.277502e-38 59019 Mir101b +Mir215 Mir215 152.78082 -3.004380 0.1939090 -15.493765 3.822341e-54 2.095542e-52 1182 Mir215 -Mir208a Mir208a 616.76981 -11.025006 0.8475353 -13.008316 1.097341e-38 5.133115e-37 4638 Mir208a +Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 -15.132265 9.922045e-52 5.137415e-50 1401 Dnm3os -Dnm3os Dnm3os 179.61643 -3.289322 0.2559302 -12.852417 8.336403e-38 3.694343e-36 1401 Dnm3os +Mir214 Mir214 134.69038 -3.216444 0.2154916 -14.926074 2.230149e-50 1.093947e-48 1048 Mir214 -Mir215 Mir215 152.78082 -3.012902 0.2351528 -12.812528 1.395132e-37 5.873506e-36 1182 Mir215 +Mir21 Mir21 26121.31011 2.963903 0.2008617 14.755939 2.817433e-49 1.312924e-47 229120 Mir21 -Mir214 Mir214 134.69038 -3.229468 0.2571076 -12.560766 3.469589e-36 1.391140e-34 1048 Mir214 +Mir1948 Mir1948 263.89527 7.074045 0.4867226 14.534039 7.374076e-48 3.272685e-46 2404 Mir1948 -Mir203 Mir203 772.92882 1.991755 0.1694325 11.755450 6.620692e-32 2.533919e-30 6739 Mir203 +Mir27b Mir27b 76478.05753 -1.904653 0.1312889 -14.507339 1.088626e-47 4.611815e-46 625308 Mir27b -Mir499 Mir499 712.45950 -11.716229 1.0177724 -11.511639 1.152660e-30 4.219739e-29 6527 Mir499 +Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 14.184987 1.134862e-45 4.598659e-44 19535 Rabggtb -Mir27b Mir27b 76478.05753 -1.906131 0.1672784 -11.394959 4.430372e-30 1.554322e-28 625308 Mir27b +Mir499 Mir499 712.45950 -10.577061 0.7528467 -14.049423 7.766426e-45 3.015962e-43 6527 Mir499 -Mir322 Mir322 899.53469 -3.147196 0.2773005 -11.349407 7.466726e-30 2.514793e-28 7074 Mir322 +Mir101b Mir101b 6846.19683 3.791681 0.2809666 13.495132 1.670548e-41 6.227801e-40 59019 Mir101b -Rabggtb Rabggtb 2257.19195 1.991117 0.1756753 11.334078 8.896442e-30 2.881079e-28 19535 Rabggtb +Mir132 Mir132 106.46062 -2.797928 0.2083376 -13.429779 4.046171e-41 1.450397e-39 857 Mir132 -Mir143hg Mir143hg 180217.77425 -2.173582 0.1966899 -11.050806 2.172555e-28 6.775153e-27 1407364 Mir143hg +Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 -12.868566 6.764677e-38 2.335066e-36 1407364 Mir143hg -Mir143 Mir143 179219.35960 -2.174835 0.1975414 -11.009513 3.438555e-28 1.034023e-26 1399819 Mir143 +Mir143 Mir143 179219.35960 -2.170303 0.1696199 -12.795094 1.746402e-37 5.813025e-36 1399819 Mir143 -Mir378 Mir378 483.21548 -3.012592 0.2747646 -10.964266 5.675913e-28 1.647972e-26 4075 Mir378 +Mir155 Mir155 57.66182 -3.788079 0.3056585 -12.393175 2.845516e-35 9.144898e-34 463 Mir155 -Mir132 Mir132 106.46062 -2.793901 0.2568175 -10.878935 1.452498e-27 4.076678e-26 857 Mir132 +Mir322 Mir322 899.53469 -3.126011 0.2622596 -11.919531 9.363380e-33 2.908890e-31 7074 Mir322 -Mir155 Mir155 57.66182 -3.815683 0.3605552 -10.582799 3.580985e-26 9.726416e-25 463 Mir155 +Mir378 Mir378 483.21548 -2.994300 0.2577321 -11.617876 3.343461e-31 1.005195e-29 4075 Mir378 -Mir24-2 Mir24-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 Mir24-2 +Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 Mir24-2 -Mir3074-2 Mir3074-2 424.48288 -2.725743 0.2589560 -10.525891 6.563718e-26 1.674743e-24 3470 Mir3074-2 +Mir3074-2 Mir3074-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 Mir3074-2 -Mir125b-2 Mir125b-2 493.08516 -2.938770 0.2803125 -10.483910 1.024200e-25 2.536401e-24 3837 Mir125b-2 +Mir199b Mir199b 47.84725 -5.294373 0.4644474 -11.399295 4.215163e-30 1.155451e-28 370 Mir199b -Mir150 Mir150 553.20599 -2.856250 0.2760016 -10.348671 4.243363e-25 1.020832e-23 4229 Mir150 +Mir802 Mir802 166.83414 8.816580 0.7782636 11.328527 9.478530e-30 2.523997e-28 1514 Mir802 -Mir182 Mir182 886.79583 5.089394 0.4937848 10.306907 6.557770e-25 1.533789e-23 7189 Mir182 +Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 -11.095122 1.324798e-28 3.429754e-27 3837 Mir125b-2 -Mir148a Mir148a 118994.46955 2.695116 0.2621094 10.282410 8.458605e-25 1.924904e-23 1002397 Mir148a +Mir301 Mir301 260.53406 -1.676984 0.1526772 -10.983852 4.570133e-28 1.151179e-26 2119 Mir301 -Mir199b Mir199b 47.84725 -5.417036 0.5304738 -10.211694 1.757697e-24 3.894687e-23 370 Mir199b +Snord104 Snord104 3851.90119 2.386573 0.2173857 10.978522 4.847915e-28 1.189015e-26 33458 Snord104 -Snord104 Snord104 3851.90119 2.396960 0.2371478 10.107451 5.119918e-24 1.105377e-22 33458 Snord104 +Mir150 Mir150 553.20599 -2.836881 0.2595088 -10.931734 8.127991e-28 1.942381e-26 4229 Mir150 -Mir193 Mir193 45.70861 5.113887 0.5386870 9.493243 2.239557e-21 4.714267e-20 421 Mir193 +Mir148a Mir148a 118994.46955 2.678852 0.2481801 10.793984 3.675045e-27 8.562855e-26 1002397 Mir148a -Mir200b Mir200b 87.13638 6.279428 0.6679043 9.401688 5.369454e-21 1.102703e-19 888 Mir200b +5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 10.506053 8.101331e-26 1.841571e-24 564 5430416N02Rik -5430416N02Rik 5430416N02Rik 62.15966 3.116558 0.3399987 9.166382 4.891610e-20 9.806514e-19 564 5430416N02Rik +Mir193 Mir193 45.70861 4.991530 0.4814098 10.368568 3.446495e-25 7.647936e-24 421 Mir193 -Mir802 Mir802 166.83414 9.771028 1.0750153 9.089199 9.977106e-20 1.953657e-18 1514 Mir802 +Mir3073 Mir3073 98.93199 8.208709 0.7944742 10.332254 5.036321e-25 1.091593e-23 904 Mir3073 -Mir125b-1 Mir125b-1 79.01988 -3.046196 0.3356809 -9.074680 1.140124e-19 2.181783e-18 609 Mir125b-1 +Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 -10.283590 8.355635e-25 1.769875e-23 609 Mir125b-1 -2610203C20Rik 2610203C20Rik 79.17666 -3.049266 0.3363186 -9.066600 1.227890e-19 2.297519e-18 610 2610203C20Rik +2610203C20Rik 2610203C20Rik 79.17666 -3.023491 0.2948614 -10.253939 1.136165e-24 2.353124e-23 610 2610203C20Rik -Snord91a Snord91a 168.95251 2.722976 0.3035329 8.970941 2.939927e-19 5.381346e-18 1437 Snord91a +Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 -9.812740 9.923710e-23 2.010630e-21 506 Mir181a-1 -Mir194-1 Mir194-1 71.10636 3.788463 0.4230333 8.955471 3.382877e-19 6.060389e-18 635 Mir194-1 +Mir184 Mir184 32.23796 -4.865023 0.4962776 -9.803028 1.092606e-22 2.166615e-21 247 Mir184 -Mir181a-1 Mir181a-1 59.53826 -3.173584 0.3580582 -8.863320 7.766622e-19 1.362395e-17 506 Mir181a-1 +Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 -9.651880 4.826276e-22 9.371019e-21 352 Mir199a-2 -Mir181a-2 Mir181a-2 347.82506 -2.863247 0.3233431 -8.855136 8.358205e-19 1.436247e-17 2817 Mir181a-2 +Mir182 Mir182 886.79583 4.919630 0.5101689 9.643140 5.255515e-22 9.996204e-21 7189 Mir182 -Mir184 Mir184 32.23796 -4.996780 0.5668564 -8.814896 1.197967e-18 2.017377e-17 247 Mir184 +Snord91a Snord91a 168.95251 2.700421 0.2835464 9.523738 1.670595e-21 3.113990e-20 1437 Snord91a -

DifferentialCounts log output

Differential images and outputs

+(Click on a thumbnail image to download the corresponding original PDF image)
+

+ + + + + + +

Image called Differential_rowsum_bar_charts.pdf

Image called Differential_venn_edgeRtest_significant_genes_overlap.pdf

+ +

Differential log output

 
-KernSmooth 2.23 loaded
+[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] @@ Total low count contigs per sample =  1,1,1,1,1,1,1,1
+
+[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
 
-Copyright M. P. Wand 1997-2009
+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] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
+
+[1] heart liver
+
+
+

+ +

Differential log output

+ +

 
 Attaching package: ‘gplots’
 
@@ -157,9 +221,9 @@
 
     lowess
 
-Loading required package: limma
+Loading required package: methods
 
-Loading required package: methods
+Loading required package: limma
 
 Loading required package: splines
 
@@ -187,7 +251,7 @@
 
 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
+    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
 
 Loading required package: IRanges
 
@@ -197,7 +261,7 @@
 
     space
 
-Loading required package: GenomeInfoDb
+Loading required package: XVector
 
 Loading required package: Rcpp
 
@@ -209,21 +273,21 @@
 
 final dispersion estimates
 
-Warning messages:
+you had estimated gene-wise dispersions, removing these
 
-1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
+you had estimated fitted dispersions, removing these
 
-  Outlier (-Inf) in boxplot 1 is not drawn
+you had estimated gene-wise dispersions, removing these
 
-2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
+you had estimated fitted dispersions, removing these
 
-  Outlier (-Inf) in boxplot 3 is not drawn
+Warning message:
 
-3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067,  :
+closing unused connection 4 (edgeR.log) 
 
-  some notches went outside hinges ('box'): maybe set notch=FALSE
+Warning message:
 
-4: In par(defpar) : calling par(new=TRUE) with no plot
+In sink() : no sink to remove

@@ -232,11 +296,11 @@ (Click on a thumbnail image to download the corresponding original PDF image)

- + - +

Image called VOOM_DifferentialCounts_mean_variance_plot.pdf

Image called VOOM_edgeRtest_mean_variance_plot.pdf

Image called VOOM_DifferentialCounts_qqplot.pdf

@@ -247,107 +311,107 @@ # VOOM top 50 - logFC AveExpr t P.Value adj.P.Val B NReads URL + Contig 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 +Mir192 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 +Mir208a 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 +Mir3073 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 +Mir802 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 +Mir208b 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 +Mir499 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 +Mir10b 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 +Mir148a 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 +Mir490 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 +Mir122a 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 +Mir133b 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 +Mir149 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 +Mir101b 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 +Mir143 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 +Mir194-2 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 +Mir23a 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 +Mir1983 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 +Mir27a 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 +Cyp3a25 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 +Mir200a 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 +Mir181d 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 +Mir153 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 +Mir204 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 +Gm5441 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 +Rabggtb 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 +Mir504 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 +Mir133a-1 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 +Mir195 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 +Mir27b 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 +Snord52 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 +Mir322 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 +Mir181c 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 +Mir1948 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 +0610031O16Rik 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 +Mir201 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 +Mir21 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 +Mir184 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 +1810019D21Rik 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 +Mir203 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 +1110038B12Rik 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 +Snord104 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 +Mir182 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 +Mir547 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 +Mir143hg 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 +Scnn1b 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 +Mir125b-2 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 +Mir1a-1 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 +Mir378 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 +Mir199b 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 +Mir155 Mir155 -4.158272 3.8002361 -9.845490 1.896814e-07 4.328530e-06 7.604112 463 Mir155 @@ -356,81 +420,37 @@ (Click on a thumbnail image to download the corresponding original PDF image)

- + - + - + - + - + - + - - - -

edgeR log output

 
-[1] Common Dispersion = 0.228651459675839 CV =  0.478175134940995 getPriorN =  3.33333333333333
+[1] Common Dispersion = 0.228651460998105 CV =  0.478175136323613 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
+[1] @@ edgeR Top tags\n
 
                        Name      logFC    logCPM        LR        PValue   adj.p.value Dispersion totreads                                                                                               URL
 
@@ -438,19 +458,19 @@
 
 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  7.737466e-93  2.942816e-90 0.10508096    14756             Mir208b
+Mir208b             Mir208b -13.291635  9.905945 417.69758  7.737463e-93  2.942815e-90 0.10508096    14756             Mir208b
 
-Mir122a             Mir122a  10.514683 12.478088 415.17429  2.740528e-92  7.817355e-90 0.10803882    90428             Mir122a
+Mir122a             Mir122a  10.514683 12.478088 415.17429  2.740525e-92  7.817349e-90 0.10803882    90428             Mir122a
 
-Mir204               Mir204  -7.498162  7.634507 341.30678  3.313429e-76  7.561245e-74 0.06907958     2601               Mir204
+Mir204               Mir204  -7.498162  7.634507 341.30678  3.313430e-76  7.561247e-74 0.06907958     2601               Mir204
 
-Mir499               Mir499 -13.577454  8.700078 325.79199  7.930762e-73  1.508166e-70 0.12042284     6527               Mir499
+Mir499               Mir499 -13.577454  8.700078 325.79199  7.930755e-73  1.508165e-70 0.12042284     6527               Mir499
 
-Mir490               Mir490  -8.534394  6.991023 303.17184  6.710365e-68  1.093790e-65 0.07949711     1741               Mir490
+Mir490               Mir490  -8.534394  6.991023 303.17184  6.710366e-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
+Mir192               Mir192   6.953853 17.169364 217.22867  3.638307e-49  5.189135e-47 0.12700995  2325567               Mir192
 
-Mir802               Mir802  11.440805  6.593380 212.88058  3.231647e-48  4.097010e-46 0.12273671     1514               Mir802
+Mir802               Mir802  11.440805  6.593380 212.88059  3.231644e-48  4.097007e-46 0.12273671     1514               Mir802
 
 Mir1948             Mir1948   7.418142  7.252734 195.66958  1.840248e-44  2.099723e-42 0.12060221     2404             Mir1948
 
@@ -458,21 +478,21 @@
 
 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  7.883296e-39  6.919108e-37 0.06368883    23605             Mir181c
+Mir181c             Mir181c  -3.767686 10.639598 169.87390  7.883295e-39  6.919107e-37 0.06368883    23605             Mir181c
 
-Mir3073             Mir3073  10.686337  5.859950 164.86740  9.778601e-38  7.969560e-36 0.14069249      904             Mir3073
+Mir3073             Mir3073  10.686337  5.859950 164.86740  9.778593e-38  7.969554e-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
+Mir10b               Mir10b  -5.182616 13.946466 147.24793  6.926819e-34  4.649118e-32 0.12268790   197340               Mir10b
 
-Mir101b             Mir101b   3.759962 11.863187 136.31359  1.703813e-31  1.080028e-29 0.07961343    59019             Mir101b
+Mir101b             Mir101b   3.759962 11.863187 136.31359  1.703812e-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
+Mir27a               Mir27a  -3.064687 10.642480 124.98911  5.117477e-29  2.919520e-27 0.06113852    21886               Mir27a
 
 Mir182               Mir182   5.057509  8.846381 123.17765  1.275060e-28  6.927826e-27 0.13653707     7189               Mir182
 
@@ -480,7 +500,7 @@
 
 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 0.06896653     2817         Mir181a-2
+Mir181a-2         Mir181a-2  -3.000177  7.637692 101.38361  7.578821e-24  3.603098e-22 0.06896654     2817         Mir181a-2
 
 Mir125b-2         Mir125b-2  -2.987759  8.144514  91.72544  9.957640e-22  4.488356e-20 0.07737381     3837         Mir125b-2
 
@@ -490,43 +510,43 @@
 
 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  5.031521e-20  1.960318e-18 0.17482280      159             Mir133b
+Mir133b             Mir133b  -8.383611  3.584760  83.96681  5.031517e-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
+Mir150               Mir150  -2.883446  8.307765  83.91918  5.154210e-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
+Mir24-2             Mir24-2  -2.778307  7.935651  83.71222  5.723024e-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
+Mir214               Mir214  -3.271172  6.271755  80.43948  2.997458e-19  9.771712e-18 0.09566584     1048               Mir214
 
-Snord104           Snord104   2.330488 11.053611  79.50529  4.809370e-19  1.524303e-17 0.05915990    33458           Snord104
+Snord104           Snord104   2.330488 11.053611  79.50529  4.809369e-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
+Mir21                 Mir21   2.923147 13.825255  75.51798  3.620938e-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
+Cyp3a25             Cyp3a25   8.681501  3.972085  72.29680  1.851471e-17  5.029829e-16 0.23125383      226             Cyp3a25
 
-Rabggtb             Rabggtb   1.934093 10.298211  72.02043  2.129809e-17  5.651423e-16 0.04596646    19535             Rabggtb
+Rabggtb             Rabggtb   1.934093 10.298211  72.02043  2.129809e-17  5.651422e-16 0.04596646    19535             Rabggtb
 
-Mir23b               Mir23b  -2.100584 10.184110  71.44225  2.854936e-17  7.403367e-16 0.05416378    16387               Mir23b
+Mir23b               Mir23b  -2.100584 10.184110  71.44225  2.854935e-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
+Snord52             Snord52   2.207491 10.217554  71.27974  3.100027e-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
+Gm5441               Gm5441  -6.881248  3.538457  70.05615  5.764004e-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
+Mir153               Mir153  -6.857671  3.517446  69.37600  8.137282e-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
 
@@ -534,28 +554,11 @@
 
 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
+[1] @@ 416 tags significant at adj p= 0.05

Other images and outputs

-(Click on a thumbnail image to download the corresponding original PDF image)
-

- - - - - - - - - -

Other log output

@@ -564,59 +567,9 @@
 
 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
+R version 3.0.2 (2013-09-25)
 
-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)
+Platform: x86_64-pc-linux-gnu (64-bit)
 
 locale:
 
@@ -628,11 +581,11 @@
 
 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          
+ [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          
 
 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       
+ [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

@@ -642,28 +595,27 @@

- - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + +

Output File Name (click to view)	Size
DESeq2.log	10.5 KB
DESeq2_DifferentialCounts_MA_plot.pdf	14.9 KB
DESeq2_DifferentialCounts_PCA_plot.pdf	4.9 KB
DESeq2_DifferentialCounts_dispersion_estimates.pdf	188.4 KB
DESeq2_DifferentialCounts_qqplot.pdf	12.8 KB
DESeq2_DifferentialCounts_sample_distance_plot.pdf	9.4 KB
DifferentialCounts.Rscript	28.4 KB
DifferentialCounts_error.log	2.0 KB
DifferentialCounts_runner.log	3.5 KB
Filtering_rowsum_bar_charts.pdf	6.3 KB
VOOM.log	9.4 KB
VOOM_DifferentialCounts_mean_variance_plot.pdf	18.3 KB
VOOM_DifferentialCounts_qqplot.pdf	17.5 KB
Venn_DifferentialCounts_significant_genes_overlap.pdf	9.7 KB
edgeR.log	13.1 KB
edgeR_DifferentialCounts_BCV_vs_abundance.pdf	17.4 KB
edgeR_DifferentialCounts_GoodnessofFit.pdf	13.1 KB
edgeR_DifferentialCounts_MDSplot.pdf	5.0 KB
edgeR_DifferentialCounts_qqplot.pdf	15.2 KB
edgeR_DifferentialCounts_raw_norm_counts_box.pdf	7.8 KB
edgeR_DifferentialCounts_smearplot.pdf	16.6 KB
edgeR_DifferentialCounts_top_100_heatmap.pdf	11.5 KB
sample_counts_histogram.pdf	11.0 KB
DESeq2_edgeRtest_MA_plot.pdf	15.0 KB
DESeq2_edgeRtest_PCA_plot.pdf	4.9 KB
DESeq2_edgeRtest_dispersion_estimates.pdf	190.6 KB
DESeq2_edgeRtest_qqplot.pdf	13.3 KB
DESeq2_edgeRtest_sample_distance_plot.pdf	9.5 KB
Differential.log	1.4 KB
Differential_Counts.Rscript	28.3 KB
Differential_Counts_error.log	1.8 KB
Differential_Counts_runner.log	1.3 KB
Differential_rowsum_bar_charts.pdf	6.3 KB
Differential_venn_edgeRtest_significant_genes_overlap.pdf	9.7 KB
VOOM.log	10.1 KB
VOOM_edgeRtest_mean_variance_plot.pdf	18.3 KB
VOOM_edgeRtest_qqplot.pdf	17.5 KB
edgeR.log	10.4 KB
edgeR_edgeRtest_BCV_vs_abundance.pdf	17.4 KB
edgeR_edgeRtest_GoodnessofFit.pdf	13.1 KB
edgeR_edgeRtest_MDSplot.pdf	4.9 KB
edgeR_edgeRtest_qqplot.pdf	15.2 KB
edgeR_edgeRtest_smearplot.pdf	16.7 KB
edgeR_edgeRtest_top_100_heatmap.pdf	11.2 KB

diff -r a95f5496d330 -r a9ffdf5f7d2a test-data/edgeRtest1out.xls --- a/test-data/edgeRtest1out.xls Fri Nov 28 06:45:33 2014 -0500 +++ b/test-data/edgeRtest1out.xls Thu Jan 01 21:53:07 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 -11.8407506325994 8.46501715136261 594.169461788588 3.10454340520719e-131 3.54228402534141e-128 0.0517121951525415 4638 0 0 0 0.539638866040004 398.994619637285 739.374891373071 901.627384247207 673.126883915814 0 0 0 1 1060 956 1693 928 -Mir149 -7.00898388335122 8.86176664758882 484.303208159111 2.47390942083987e-107 1.41136532458914e-104 0.0495993679492896 6164 18.1338061399734 6.7041218845597 4.90063242902982 5.93467521388658 754.954773589966 422.708450804407 1774.96378211422 686.472355755848 25 9 8 16 1399 1123 2295 1289 -Mir208b -13.2916347677151 9.90594480087289 417.697578727504 7.73746551125031e-93 2.94281604944553e-90 0.105080963479123 14756 0.773404698088987 0 0 0 1255.17448088526 610.90062982945 4804.9444632202 811.163589922971 1 0 0 0 2049 1647 8904 2155 -Mir122a 10.5146833712803 12.4780878408673 415.174286432694 2.74052770257465e-92 7.81735527159419e-90 0.108038824620343 90428 21591.5602947436 18051.2206253928 7296.42910777178 9073.74748483171 6.47566639248005 2.63487012968019 20.8819268484026 4.26049561369029 29767 24233 11911 24463 12 7 27 8 -Mir204 -7.49816212336048 7.63450677628189 341.306784912854 3.31342909192416e-76 7.56124518777094e-74 0.0690795842951528 2601 3.06289526814364 0.741834401735822 0.539638866040004 3.38769016673167 441.614082608811 292.376511489496 669.500122687819 402.9922155052 5 2 1 9 571 549 923 541 -Mir499 -13.5774541855868 8.70007828481468 325.791991149153 7.93076155694377e-73 1.50816648941214e-70 0.120422839284927 6527 0 0 0 0 630.331101425477 543.778775080954 2540.36533539833 289.686333877839 0 0 0 0 869 730 4147 781 -Mir490 -8.53439419160321 6.99102321339932 303.171840011248 6.71036527101623e-68 1.09378953917565e-65 0.0794971088607054 1741 1.11275160260373 0.539638866040004 0 0.773404698088987 187.994368954084 225.58454838127 558.676823713309 197.25045526845 3 1 0 1 353 311 750 322 -Mir192 6.95385326892823 17.1693636192881 217.228663189203 3.63831152188904e-49 5.18914180809424e-47 0.127009950205414 2325567 480279.658435161 365245.774587834 386444.883402629 195324.997977042 1734.39931545257 1190.58488859692 4662.8569247785 1731.8914669651 662133 490327 630849 526600 3214 3163 6029 3252 -Mir802 11.4408053854895 6.59338011170441 212.880584185723 3.23164660393739e-48 4.09700975010284e-46 0.122736709116123 1514 297.880654054082 150.940417428822 161.641581900598 187.461807002373 0 0 0 0 552 401 209 352 0 0 0 0 -Mir1948 7.41814210391099 7.25273383973858 195.669583395952 1.84024805337572e-44 2.0997230289017e-42 0.120602206022636 2404 672.088682639329 345.100144708913 187.866231610125 459.604800308149 1.22515810725746 0.741834401735822 1.61891659812001 1.50564007410296 869 648 259 617 2 2 3 4 -Mir194-2 5.2989500004112 7.81152218291727 191.855876570524 1.25095983644798e-43 1.29758652126104e-41 0.0867075108051565 3570 954.563555208202 644.340603349349 268.922204543012 326.407136763762 10.2531384547601 5.64615027788611 15.4680939617797 8.52099122738058 1316 865 439 880 19 15 20 16 -Mir23a -3.15380742698008 9.52940174927932 177.531847119581 1.67624841439969e-40 1.59383286735837e-38 0.0444276305914111 10118 161.348982377541 123.577300323161 82.0573840386115 252.903336275099 1029.97481460963 1168.54246765989 2652.59755899079 1104.4800336926 435 229 218 327 1934 1611 3561 1803 -Mir181c -3.76768628525163 10.6395980992134 169.873900900084 7.88329624570189e-39 6.9191084741122e-37 0.0636888302557337 23605 213.424480504095 283.066119500569 204.503789457134 309.725408870746 2598.21968148269 1906.95859394623 4385.72498306218 1854.19914371345 567 366 384 427 3488 3113 11824 3436 -Mir3073 10.6863366383693 5.85995006147614 164.867397698648 9.77860110098025e-38 7.96955989729891e-36 0.140692488968037 904 208.889457287396 80.8599497892047 70.6926914512405 80.5517439645085 0 0 0 0 341 218 131 214 0 0 0 0 -Mir181d -3.64396314911003 7.30037121099239 162.185914136024 3.76766286785041e-37 2.86593555481154e-35 0.0572957439778929 2139 36.7547432177237 15.5785224364523 24.8233878378402 14.3035807039781 321.736354405019 181.071063581837 559.246581356781 317.328435869159 60 42 46 38 416 340 771 426 -Mir195 -3.20368283579531 8.21508892700014 150.205483553103 1.56331363569556e-34 1.11483803645539e-32 0.0523501993564209 3962 114.605654804632 83.4290723411874 45.9434290221546 44.5100641041494 418.220121181003 260.475732819813 957.475016234166 421.789065755339 158 112 75 120 775 692 1238 792 -Mir10b -5.18261587718538 13.9464657676444 147.2479242931 6.92682218855341e-34 4.64912006890556e-32 0.122687897974268 197340 1838.96231899344 400.590576937344 641.630611721565 668.880602920241 26812.394073349 28809.4713397737 37624.0209792169 36990.364949274 3002 1080 1189 1777 34668 54096 51870 49658 -Mir101b 3.75996221155207 11.8631868690484 136.313585748544 1.70381275861018e-31 1.08002797643012e-29 0.0796134341467803 59019 9087.10458204967 8026.74794979784 12106.8992210832 6677.72426360676 235.532422551124 293.563543125762 746.79747675507 443.160892004989 17063 11066 16253 10901 635 544 1984 573 -Mir378 -3.11559944052991 8.11961743410334 126.764083280248 2.09223317990255e-29 1.25644108329937e-27 0.0594239119360556 4075 74.4701635135206 33.8769016673167 95.1287778649454 56.4515668813963 441.014165324154 420.869873864026 1164.51278094821 201.778957272144 138 90 123 106 608 565 1901 544 -Mir27a -3.06468708614915 10.642480146578 124.989109557168 5.11747734797658e-29 2.91952082702064e-27 0.0611385232589585 21886 352.000423623648 338.893207873123 150.564007410296 587.78757054763 2135.04086441055 2602.56385720899 5711.91184564487 2379.25704429398 949 628 400 760 4009 3588 7668 3884 -Mir182 5.05750948040129 8.84638119837792 123.177648891378 1.27505991541255e-28 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