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comparison test-data/edgeRtest1out.html @ 132:0de946608423 draft

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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
2 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
3 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
4 <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://getgalaxy.org/" />
5 <title></title>
6 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
7 </head>
8 <body>
9 <div class="toolFormBody">
10
11 <div class="infomessage">Galaxy Tool "Differential_Counts" run at 28/12/2014 21:02:37</div><br/>
12 <div class="toolFormTitle">DESeq2 images and outputs</div>
13 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
14 <div><table class="simple" cellpadding="2" cellspacing="2">
15 <tr>
16 <td><a href="DESeq2_edgeRtest_MA_plot.pdf"><img src="DESeq2_edgeRtest_MA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_MA_plot.pdf" hspace="5" width="400"
17 alt="Image called DESeq2_edgeRtest_MA_plot.pdf"/></a></td>
18
19 <td><a href="DESeq2_edgeRtest_PCA_plot.pdf"><img src="DESeq2_edgeRtest_PCA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_PCA_plot.pdf" hspace="5" width="400"
20 alt="Image called DESeq2_edgeRtest_PCA_plot.pdf"/></a></td>
21
22 <td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf"><img src="DESeq2_edgeRtest_dispersion_estimates.png" title="Click to download a PDF of DESeq2_edgeRtest_dispersion_estimates.pdf" hspace="5" width="400"
23 alt="Image called DESeq2_edgeRtest_dispersion_estimates.pdf"/></a></td>
24 </tr>
25 <tr>
26 <td><a href="DESeq2_edgeRtest_qqplot.pdf"><img src="DESeq2_edgeRtest_qqplot.png" title="Click to download a PDF of DESeq2_edgeRtest_qqplot.pdf" hspace="5" width="400"
27 alt="Image called DESeq2_edgeRtest_qqplot.pdf"/></a></td>
28
29 <td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf"><img src="DESeq2_edgeRtest_sample_distance_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_sample_distance_plot.pdf" hspace="5" width="400"
30 alt="Image called DESeq2_edgeRtest_sample_distance_plot.pdf"/></a></td>
31
32 <td>&nbsp;</td>
33 </tr></table></div>
34
35 <div class="toolFormTitle">DESeq2 log output</div>
36
37 <pre>
38
39 # DESeq top 50
40
41 Contig baseMean log2FoldChange lfcSE stat pvalue padj NReads URL
42
43 Mir192 Mir192 271352.97636 6.965264 0.2150593 32.387646 4.096935e-230 3.818343e-227 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
44
45 Mir122a Mir122a 10112.31117 10.312083 0.3292695 31.318061 2.649329e-215 1.234587e-212 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
46
47 Mir149 Mir149 810.35429 -6.911118 0.2341392 -29.517132 1.735536e-191 5.391733e-189 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
48
49 Mir23a Mir23a 1289.18043 -3.104086 0.1191688 -26.047815 1.424245e-149 3.318491e-147 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
50
51 Mir181d Mir181d 275.22797 -3.581172 0.1778187 -20.139461 3.329373e-90 6.205952e-88 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
52
53 Mir204 Mir204 347.57397 -7.284200 0.3771119 -19.315751 3.959346e-83 6.150183e-81 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
54
55 Mir23b Mir23b 2028.55377 -2.065110 0.1085802 -19.019217 1.182361e-80 1.574229e-78 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
56
57 Mir27a Mir27a 2788.72629 -3.016676 0.1688167 -17.869539 2.036708e-71 2.372765e-69 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
58
59 Mir195 Mir195 519.86200 -3.152795 0.1784796 -17.664734 7.838131e-70 8.116820e-68 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
60
61 Mir194-2 Mir194-2 391.65678 5.222911 0.3099275 16.852045 1.013492e-63 9.445744e-62 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
62
63 Mir208b Mir208b 1649.77924 -11.396172 0.6771238 -16.830264 1.464482e-63 1.240816e-61 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
64
65 Mir10b Mir10b 27820.40551 -5.071453 0.3044884 -16.655656 2.753110e-62 2.138249e-60 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
66
67 Mir181c Mir181c 2765.96510 -3.660964 0.2275711 -16.087120 3.141152e-58 2.251965e-56 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
68
69 Mir208a Mir208a 616.76981 -10.356524 0.6559218 -15.789267 3.688391e-56 2.455415e-54 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
70
71 Mir490 Mir490 220.99790 -8.059660 0.5142876 -15.671504 2.369067e-55 1.471980e-53 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
72
73 Mir203 Mir203 772.92882 1.990849 0.1274099 15.625546 4.877239e-55 2.840992e-53 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
74
75 Mir215 Mir215 152.78082 -3.004380 0.1939090 -15.493765 3.822341e-54 2.095542e-52 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
76
77 Dnm3os Dnm3os 179.61643 -3.278392 0.2166491 -15.132265 9.922045e-52 5.137415e-50 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
78
79 Mir214 Mir214 134.69038 -3.216444 0.2154916 -14.926074 2.230149e-50 1.093947e-48 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
80
81 Mir21 Mir21 26121.31011 2.963903 0.2008617 14.755939 2.817433e-49 1.312924e-47 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
82
83 Mir1948 Mir1948 263.89527 7.074045 0.4867226 14.534039 7.374076e-48 3.272685e-46 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
84
85 Mir27b Mir27b 76478.05753 -1.904653 0.1312889 -14.507339 1.088626e-47 4.611815e-46 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
86
87 Rabggtb Rabggtb 2257.19195 1.988368 0.1401741 14.184987 1.134862e-45 4.598659e-44 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
88
89 Mir499 Mir499 712.45950 -10.577061 0.7528467 -14.049423 7.766426e-45 3.015962e-43 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
90
91 Mir101b Mir101b 6846.19683 3.791681 0.2809666 13.495132 1.670548e-41 6.227801e-40 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
92
93 Mir132 Mir132 106.46062 -2.797928 0.2083376 -13.429779 4.046171e-41 1.450397e-39 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
94
95 Mir143hg Mir143hg 180217.77425 -2.169143 0.1685614 -12.868566 6.764677e-38 2.335066e-36 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
96
97 Mir143 Mir143 179219.35960 -2.170303 0.1696199 -12.795094 1.746402e-37 5.813025e-36 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
98
99 Mir155 Mir155 57.66182 -3.788079 0.3056585 -12.393175 2.845516e-35 9.144898e-34 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
100
101 Mir322 Mir322 899.53469 -3.126011 0.2622596 -11.919531 9.363380e-33 2.908890e-31 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
102
103 Mir378 Mir378 483.21548 -2.994300 0.2577321 -11.617876 3.343461e-31 1.005195e-29 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
104
105 Mir24-2 Mir24-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
106
107 Mir3074-2 Mir3074-2 424.48288 -2.712674 0.2361028 -11.489378 1.491830e-30 4.213289e-29 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
108
109 Mir199b Mir199b 47.84725 -5.294373 0.4644474 -11.399295 4.215163e-30 1.155451e-28 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
110
111 Mir802 Mir802 166.83414 8.816580 0.7782636 11.328527 9.478530e-30 2.523997e-28 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
112
113 Mir125b-2 Mir125b-2 493.08516 -2.919341 0.2631193 -11.095122 1.324798e-28 3.429754e-27 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
114
115 Mir301 Mir301 260.53406 -1.676984 0.1526772 -10.983852 4.570133e-28 1.151179e-26 2119 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a>
116
117 Snord104 Snord104 3851.90119 2.386573 0.2173857 10.978522 4.847915e-28 1.189015e-26 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
118
119 Mir150 Mir150 553.20599 -2.836881 0.2595088 -10.931734 8.127991e-28 1.942381e-26 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
120
121 Mir148a Mir148a 118994.46955 2.678852 0.2481801 10.793984 3.675045e-27 8.562855e-26 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
122
123 5430416N02Rik 5430416N02Rik 62.15966 3.089960 0.2941123 10.506053 8.101331e-26 1.841571e-24 564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
124
125 Mir193 Mir193 45.70861 4.991530 0.4814098 10.368568 3.446495e-25 7.647936e-24 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
126
127 Mir3073 Mir3073 98.93199 8.208709 0.7944742 10.332254 5.036321e-25 1.091593e-23 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
128
129 Mir125b-1 Mir125b-1 79.01988 -3.020660 0.2937360 -10.283590 8.355635e-25 1.769875e-23 609 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
130
131 2610203C20Rik 2610203C20Rik 79.17666 -3.023491 0.2948614 -10.253939 1.136165e-24 2.353124e-23 610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
132
133 Mir181a-1 Mir181a-1 59.53826 -3.151487 0.3211628 -9.812740 9.923710e-23 2.010630e-21 506 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
134
135 Mir184 Mir184 32.23796 -4.865023 0.4962776 -9.803028 1.092606e-22 2.166615e-21 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
136
137 Mir199a-2 Mir199a-2 44.84878 -3.422216 0.3545647 -9.651880 4.826276e-22 9.371019e-21 352 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a>
138
139 Mir182 Mir182 886.79583 4.919630 0.5101689 9.643140 5.255515e-22 9.996204e-21 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
140
141 Snord91a Snord91a 168.95251 2.700421 0.2835464 9.523738 1.670595e-21 3.113990e-20 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
142
143
144 </pre>
145
146 <div class="toolFormTitle">Differential images and outputs</div>
147 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
148 <div><table class="simple" cellpadding="2" cellspacing="2">
149 <tr>
150 <td><a href="Differential_rowsum_bar_charts.pdf"><img src="Differential_rowsum_bar_charts.png" title="Click to download a PDF of Differential_rowsum_bar_charts.pdf" hspace="5" width="400"
151 alt="Image called Differential_rowsum_bar_charts.pdf"/></a></td>
152
153 <td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf"><img src="Differential_venn_edgeRtest_significant_genes_overlap.png" title="Click to download a PDF of Differential_venn_edgeRtest_significant_genes_overlap.pdf" hspace="5" width="400"
154 alt="Image called Differential_venn_edgeRtest_significant_genes_overlap.pdf"/></a></td>
155 </tr>
156
157 </table></div>
158
159 <div class="toolFormTitle">Differential log output</div>
160
161 <pre>
162
163 [1] @@@ Quantiles for non-zero row counts:
164
165 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
166
167 1.0 1.0 2.0 3.0 4.0 8.0 13.0 24.0 86.6 753.0 2325567.0
168
169 [1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
170
171 [1] "@@ using genecards substitution for urls"
172
173 [1] @@ Total low count contigs per sample = 1,1,1,1,1,1,1,1
174
175 [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
176
177 [1] Using design matrix:
178
179 (Intercept) groupliver
180
181 1 1 1
182
183 2 1 1
184
185 3 1 1
186
187 4 1 1
188
189 5 1 0
190
191 6 1 0
192
193 7 1 0
194
195 8 1 0
196
197 attr(,"assign")
198
199 [1] 0 1
200
201 attr(,"contrasts")
202
203 attr(,"contrasts")$group
204
205 [1] contr.treatment
206
207 [1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
208
209 [1] heart liver
210
211
212 </pre>
213
214 <div class="toolFormTitle">Differential log output</div>
215
216 <pre>
217
218 Attaching package: ‘gplots’
219
220 The following object is masked from ‘package:stats’:
221
222 lowess
223
224 Loading required package: methods
225
226 Loading required package: limma
227
228 Loading required package: splines
229
230 Loading required package: DESeq2
231
232 Loading required package: GenomicRanges
233
234 Loading required package: BiocGenerics
235
236 Loading required package: parallel
237
238 Attaching package: ‘BiocGenerics’
239
240 The following objects are masked from ‘package:parallel’:
241
242 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
243
244 The following object is masked from ‘package:limma’:
245
246 plotMA
247
248 The following object is masked from ‘package:stats’:
249
250 xtabs
251
252 The following objects are masked from ‘package:base’:
253
254 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
255
256 Loading required package: IRanges
257
258 Attaching package: ‘IRanges’
259
260 The following object is masked from ‘package:gplots’:
261
262 space
263
264 Loading required package: XVector
265
266 Loading required package: Rcpp
267
268 Loading required package: RcppArmadillo
269
270 gene-wise dispersion estimates
271
272 mean-dispersion relationship
273
274 final dispersion estimates
275
276 you had estimated gene-wise dispersions, removing these
277
278 you had estimated fitted dispersions, removing these
279
280 you had estimated gene-wise dispersions, removing these
281
282 you had estimated fitted dispersions, removing these
283
284 Warning message:
285
286 closing unused connection 4 (edgeR.log)
287
288 Warning message:
289
290 In sink() : no sink to remove
291
292
293 </pre>
294
295 <div class="toolFormTitle">VOOM images and outputs</div>
296 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
297 <div><table class="simple" cellpadding="2" cellspacing="2">
298 <tr>
299 <td><a href="VOOM_edgeRtest_mean_variance_plot.pdf"><img src="VOOM_edgeRtest_mean_variance_plot.png" title="Click to download a PDF of VOOM_edgeRtest_mean_variance_plot.pdf" hspace="5" width="400"
300 alt="Image called VOOM_edgeRtest_mean_variance_plot.pdf"/></a></td>
301
302 <td><a href="VOOM_edgeRtest_qqplot.pdf"><img src="VOOM_edgeRtest_qqplot.png" title="Click to download a PDF of VOOM_edgeRtest_qqplot.pdf" hspace="5" width="400"
303 alt="Image called VOOM_edgeRtest_qqplot.pdf"/></a></td>
304 </tr>
305
306 </table></div>
307
308 <div class="toolFormTitle">VOOM log output</div>
309
310 <pre>
311
312 # VOOM top 50
313
314 Contig logFC AveExpr t P.Value adj.P.Val B NReads URL
315
316 Mir192 Mir192 6.689950 14.4417888 50.335160 1.802287e-16 2.056409e-13 27.414844 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
317
318 Mir208a Mir208a -10.458438 3.8918506 -29.183545 2.249812e-13 1.283518e-10 19.141041 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
319
320 Mir3073 Mir3073 8.318578 2.6485638 25.821264 1.102217e-12 4.192097e-10 18.063600 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
321
322 Mir802 Mir802 8.992449 2.9857711 25.195575 1.514327e-12 4.319618e-10 17.906674 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
323
324 Mir208b Mir208b -12.256447 4.4678897 -22.360114 7.074494e-12 1.614400e-09 16.920424 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
325
326 Mir499 Mir499 -11.104485 3.8066799 -21.990054 8.769804e-12 1.667724e-09 16.728874 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
327
328 Mir10b Mir10b -4.775768 12.4173688 -21.487387 1.180685e-11 1.924516e-09 17.249348 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
329
330 Mir148a Mir148a 2.751538 15.4237642 20.289553 2.464883e-11 3.515539e-09 16.455471 1002397 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
331
332 Mir490 Mir490 -8.497742 3.6613221 -18.336110 8.980482e-11 1.138526e-08 13.923237 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
333
334 Mir122a Mir122a 10.197963 8.1512374 17.467826 1.663427e-10 1.897970e-08 14.215445 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
335
336 Mir133b Mir133b -6.172367 1.3497975 -17.274094 1.916064e-10 1.987481e-08 13.840201 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
337
338 Mir149 Mir149 -7.041176 6.0886889 -16.861286 2.602547e-10 2.474589e-08 13.714880 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
339
340 Mir101b Mir101b 3.837883 10.6216725 15.443054 7.873164e-10 6.910215e-08 13.054350 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
341
342 Mir143 Mir143 -1.912927 16.0353646 -14.922755 1.209475e-09 9.857220e-08 12.374988 1399819 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
343
344 Mir194-2 Mir194-2 5.534694 6.2627211 14.703097 1.455682e-09 1.107289e-07 12.316769 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
345
346 Mir23a Mir23a -2.905961 8.6431895 -14.558394 1.646894e-09 1.174441e-07 12.339306 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
347
348 Mir1983 Mir1983 -5.612359 1.1061384 -14.266537 2.119488e-09 1.422551e-07 11.743589 101 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
349
350 Mir27a Mir27a -2.849084 10.0939084 -14.158498 2.329669e-09 1.476752e-07 11.960195 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
351
352 Cyp3a25 Cyp3a25 6.312461 1.6425308 13.845627 3.074630e-09 1.846396e-07 11.502713 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
353
354 Mir200a Mir200a 6.129125 1.8320913 13.226966 5.410979e-09 3.086963e-07 10.979834 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
355
356 Mir181d Mir181d -3.405544 6.3702152 -13.064584 6.300369e-09 3.423201e-07 11.006301 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
357
358 Mir153 Mir153 -5.698257 1.5328802 -12.832092 7.856705e-09 3.829623e-07 10.583835 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
359
360 Mir204 Mir204 -7.718081 4.5031856 -12.808496 8.036265e-09 3.829623e-07 10.353229 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
361
362 Gm5441 Gm5441 -5.716851 1.5430406 -12.806028 8.055298e-09 3.829623e-07 10.562881 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
363
364 Rabggtb Rabggtb 2.327908 9.9369857 12.760291 8.416902e-09 3.841474e-07 10.654006 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
365
366 Mir504 Mir504 -5.122304 0.8161671 -12.391521 1.205304e-08 5.289430e-07 10.144865 69 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
367
368 Mir133a-1 Mir133a-1 -4.912497 0.7297882 -12.335045 1.274466e-08 5.385801e-07 10.076395 60 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
369
370 Mir195 Mir195 -2.954216 7.3530970 -12.081859 1.641098e-08 6.603731e-07 10.055879 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
371
372 Mir27b Mir27b -1.496991 14.9464877 -12.059553 1.678424e-08 6.603731e-07 9.674850 625308 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
373
374 Snord52 Snord52 2.631712 9.7652181 11.922618 1.928407e-08 7.334374e-07 9.811774 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
375
376 Mir322 Mir322 -3.029558 8.1188344 -11.736839 2.333148e-08 8.587488e-07 9.679815 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
377
378 Mir181c Mir181c -3.676262 9.6244506 -11.575598 2.758358e-08 9.835271e-07 9.453057 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
379
380 Mir1948 Mir1948 7.101780 4.7821564 11.471202 3.077353e-08 1.033009e-06 9.233632 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
381
382 0610031O16Rik 0610031O16Rik 4.519875 0.7388871 11.470939 3.078205e-08 1.033009e-06 9.284014 78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
383
384 Mir201 Mir201 -4.964105 0.7490919 -11.289794 3.729283e-08 1.210650e-06 9.114028 63 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir201'>Mir201</a>
385
386 Mir21 Mir21 2.746616 13.2835800 11.267331 3.819755e-08 1.210650e-06 8.925217 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
387
388 Mir184 Mir184 -5.569565 2.3521173 -11.190343 4.148052e-08 1.279170e-06 8.854599 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
389
390 1810019D21Rik 1810019D21Rik 5.164581 1.0784751 11.082009 4.662057e-08 1.399844e-06 8.951908 117 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1810019D21Rik'>1810019D21Rik</a>
391
392 Mir203 Mir203 2.216791 8.5426169 10.866758 5.896538e-08 1.725115e-06 8.715639 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
393
394 1110038B12Rik 1110038B12Rik 2.383720 10.6847245 10.832157 6.125623e-08 1.744094e-06 8.573067 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
395
396 Snord104 Snord104 2.571210 10.4798167 10.811468 6.267120e-08 1.744094e-06 8.561110 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
397
398 Mir182 Mir182 5.196800 7.2088299 10.640454 7.579543e-08 2.021320e-06 8.545839 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
399
400 Mir547 Mir547 -4.542934 0.5799793 -10.635980 7.617593e-08 2.021320e-06 8.435473 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir547'>Mir547</a>
401
402 Mir143hg Mir143hg -2.291921 16.3789153 -10.597275 7.955395e-08 2.062978e-06 7.952584 1407364 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
403
404 Scnn1b Scnn1b -4.541403 0.5700621 -10.243065 1.190487e-07 3.018546e-06 8.023327 45 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scnn1b'>Scnn1b</a>
405
406 Mir125b-2 Mir125b-2 -2.896115 7.2737925 -10.091091 1.420082e-07 3.522420e-06 7.876068 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
407
408 Mir1a-1 Mir1a-1 -4.402568 0.4498447 -9.950346 1.675164e-07 4.066729e-06 7.692790 42 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-1'>Mir1a-1</a>
409
410 Mir378 Mir378 -2.733247 7.2964165 -9.922980 1.730212e-07 4.112858e-06 7.672216 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
411
412 Mir199b Mir199b -5.651345 2.8029895 -9.883978 1.812024e-07 4.219426e-06 7.548022 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
413
414 Mir155 Mir155 -4.158272 3.8002361 -9.845490 1.896814e-07 4.328530e-06 7.604112 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
415
416
417 </pre>
418
419 <div class="toolFormTitle">edgeR images and outputs</div>
420 (Click on a thumbnail image to download the corresponding original PDF image)<br/>
421 <div><table class="simple" cellpadding="2" cellspacing="2">
422 <tr>
423 <td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf"><img src="edgeR_edgeRtest_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400"
424 alt="Image called edgeR_edgeRtest_BCV_vs_abundance.pdf"/></a></td>
425
426 <td><a href="edgeR_edgeRtest_GoodnessofFit.pdf"><img src="edgeR_edgeRtest_GoodnessofFit.png" title="Click to download a PDF of edgeR_edgeRtest_GoodnessofFit.pdf" hspace="5" width="400"
427 alt="Image called edgeR_edgeRtest_GoodnessofFit.pdf"/></a></td>
428
429 <td><a href="edgeR_edgeRtest_MDSplot.pdf"><img src="edgeR_edgeRtest_MDSplot.png" title="Click to download a PDF of edgeR_edgeRtest_MDSplot.pdf" hspace="5" width="400"
430 alt="Image called edgeR_edgeRtest_MDSplot.pdf"/></a></td>
431 </tr>
432 <tr>
433 <td><a href="edgeR_edgeRtest_qqplot.pdf"><img src="edgeR_edgeRtest_qqplot.png" title="Click to download a PDF of edgeR_edgeRtest_qqplot.pdf" hspace="5" width="400"
434 alt="Image called edgeR_edgeRtest_qqplot.pdf"/></a></td>
435
436 <td><a href="edgeR_edgeRtest_smearplot.pdf"><img src="edgeR_edgeRtest_smearplot.png" title="Click to download a PDF of edgeR_edgeRtest_smearplot.pdf" hspace="5" width="400"
437 alt="Image called edgeR_edgeRtest_smearplot.pdf"/></a></td>
438
439 <td><a href="edgeR_edgeRtest_top_100_heatmap.pdf"><img src="edgeR_edgeRtest_top_100_heatmap.png" title="Click to download a PDF of edgeR_edgeRtest_top_100_heatmap.pdf" hspace="5" width="400"
440 alt="Image called edgeR_edgeRtest_top_100_heatmap.pdf"/></a></td>
441 </tr>
442
443 </table></div>
444
445 <div class="toolFormTitle">edgeR log output</div>
446
447 <pre>
448
449 [1] Common Dispersion = 0.228651460998105 CV = 0.478175136323613 getPriorN = 3.33333333333333
450
451 [1] "No GLM fit outlier genes found\n"
452
453 [1] @@ edgeR Top tags\n
454
455 Name logFC logCPM LR PValue adj.p.value Dispersion totreads URL
456
457 Mir208a Mir208a -11.840751 8.465017 594.16946 3.104543e-131 3.542284e-128 0.05171220 4638 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
458
459 Mir149 Mir149 -7.008984 8.861767 484.30321 2.473909e-107 1.411365e-104 0.04959937 6164 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
460
461 Mir208b Mir208b -13.291635 9.905945 417.69758 7.737463e-93 2.942815e-90 0.10508096 14756 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
462
463 Mir122a Mir122a 10.514683 12.478088 415.17429 2.740525e-92 7.817349e-90 0.10803882 90428 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
464
465 Mir204 Mir204 -7.498162 7.634507 341.30678 3.313430e-76 7.561247e-74 0.06907958 2601 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
466
467 Mir499 Mir499 -13.577454 8.700078 325.79199 7.930755e-73 1.508165e-70 0.12042284 6527 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
468
469 Mir490 Mir490 -8.534394 6.991023 303.17184 6.710366e-68 1.093790e-65 0.07949711 1741 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
470
471 Mir192 Mir192 6.953853 17.169364 217.22867 3.638307e-49 5.189135e-47 0.12700995 2325567 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
472
473 Mir802 Mir802 11.440805 6.593380 212.88059 3.231644e-48 4.097007e-46 0.12273671 1514 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
474
475 Mir1948 Mir1948 7.418142 7.252734 195.66958 1.840248e-44 2.099723e-42 0.12060221 2404 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
476
477 Mir194-2 Mir194-2 5.298950 7.811522 191.85588 1.250960e-43 1.297587e-41 0.08670751 3570 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
478
479 Mir23a Mir23a -3.153807 9.529402 177.53185 1.676248e-40 1.593833e-38 0.04442763 10118 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
480
481 Mir181c Mir181c -3.767686 10.639598 169.87390 7.883295e-39 6.919107e-37 0.06368883 23605 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
482
483 Mir3073 Mir3073 10.686337 5.859950 164.86740 9.778593e-38 7.969554e-36 0.14069249 904 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
484
485 Mir181d Mir181d -3.643963 7.300371 162.18591 3.767663e-37 2.865936e-35 0.05729574 2139 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
486
487 Mir195 Mir195 -3.203683 8.215089 150.20548 1.563314e-34 1.114838e-32 0.05235020 3962 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
488
489 Mir10b Mir10b -5.182616 13.946466 147.24793 6.926819e-34 4.649118e-32 0.12268790 197340 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
490
491 Mir101b Mir101b 3.759962 11.863187 136.31359 1.703812e-31 1.080028e-29 0.07961343 59019 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
492
493 Mir378 Mir378 -3.115599 8.119617 126.76408 2.092233e-29 1.256441e-27 0.05942391 4075 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
494
495 Mir27a Mir27a -3.064687 10.642480 124.98911 5.117477e-29 2.919520e-27 0.06113852 21886 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
496
497 Mir182 Mir182 5.057509 8.846381 123.17765 1.275060e-28 6.927826e-27 0.13653707 7189 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
498
499 Mir322 Mir322 -3.194159 9.012888 107.34926 3.732413e-25 1.935765e-23 0.07536483 7074 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
500
501 Mir199b Mir199b -5.520119 4.792610 102.10724 5.259607e-24 2.609223e-22 0.13417024 370 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
502
503 Mir181a-2 Mir181a-2 -3.000177 7.637692 101.38361 7.578821e-24 3.603098e-22 0.06896654 2817 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
504
505 Mir125b-2 Mir125b-2 -2.987759 8.144514 91.72544 9.957640e-22 4.488356e-20 0.07737381 3837 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
506
507 Dnm3os Dnm3os -3.331215 6.686950 91.67250 1.022763e-21 4.488356e-20 0.08810497 1401 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
508
509 Mir184 Mir184 -5.111350 4.234160 84.35542 4.133639e-20 1.686711e-18 0.13502324 247 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
510
511 Mir215 Mir215 -3.058208 6.447966 84.35278 4.139167e-20 1.686711e-18 0.08138517 1182 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
512
513 Mir133b Mir133b -8.383611 3.584760 83.96681 5.031517e-20 1.960318e-18 0.17482280 159 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
514
515 Mir150 Mir150 -2.883446 8.307765 83.91918 5.154210e-20 1.960318e-18 0.08008123 4229 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
516
517 Mir3074-2 Mir3074-2 -2.778308 7.935651 83.74839 5.619282e-20 2.040616e-18 0.07424646 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
518
519 Mir24-2 Mir24-2 -2.778307 7.935651 83.71222 5.723024e-20 2.040616e-18 0.07427992 3470 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
520
521 Mir193 Mir193 5.176579 4.801090 83.19222 7.445011e-20 2.574169e-18 0.14794861 421 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
522
523 Scarna17 Scarna17 2.182159 9.244479 81.91330 1.421894e-19 4.771710e-18 0.04982909 9224 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a>
524
525 Mir214 Mir214 -3.271172 6.271755 80.43948 2.997458e-19 9.771712e-18 0.09566584 1048 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
526
527 Snord104 Snord104 2.330488 11.053611 79.50529 4.809369e-19 1.524303e-17 0.05915990 33458 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
528
529 Mir200a Mir200a 7.201555 4.139422 77.35503 1.428304e-18 4.365755e-17 0.19287764 264 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
530
531 Mir200b Mir200b 6.525423 5.752604 77.31985 1.453976e-18 4.365755e-17 0.26237966 888 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
532
533 Mir21 Mir21 2.923147 13.825255 75.51798 3.620938e-18 1.059357e-16 0.09395834 229120 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
534
535 Mir203 Mir203 1.956427 8.767610 75.17870 4.299815e-18 1.226522e-16 0.04381710 6739 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
536
537 Mir155 Mir155 -3.886731 5.068563 73.81316 8.587210e-18 2.389758e-16 0.12522673 463 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
538
539 Cyp3a25 Cyp3a25 8.681501 3.972085 72.29680 1.851471e-17 5.029829e-16 0.23125383 226 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
540
541 Rabggtb Rabggtb 1.934093 10.298211 72.02043 2.129809e-17 5.651422e-16 0.04596646 19535 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
542
543 Mir23b Mir23b -2.100584 10.184110 71.44225 2.854935e-17 7.403367e-16 0.05416378 16387 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
544
545 Snord52 Snord52 2.207491 10.217554 71.27974 3.100027e-17 7.860292e-16 0.05941483 18059 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
546
547 Gm5441 Gm5441 -6.881248 3.538457 70.05615 5.764004e-17 1.429724e-15 0.20097284 142 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
548
549 Mir153 Mir153 -6.857671 3.517446 69.37600 8.137282e-17 1.975455e-15 0.20158808 140 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
550
551 Mir132 Mir132 -2.858294 5.938312 64.52507 9.531204e-16 2.265647e-14 0.09274248 857 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
552
553 1110038B12Rik 1110038B12Rik 2.195962 11.253090 62.92015 2.152583e-15 5.012443e-14 0.06712174 37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
554
555 Snord91a Snord91a 2.654072 6.557504 62.40549 2.795431e-15 6.379174e-14 0.08637410 1437 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
556
557 [1] @@ 416 tags significant at adj p= 0.05
558
559
560 </pre>
561
562 <div class="toolFormTitle">Other log output</div>
563
564 <pre>
565
566 ## Toolfactory generated command line = Rscript - None None
567
568 Got TCols=1 5 6 7; CCols=2 3 4 8
569
570 R version 3.0.2 (2013-09-25)
571
572 Platform: x86_64-pc-linux-gnu (64-bit)
573
574 locale:
575
576 [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
577
578 attached base packages:
579
580 [1] parallel splines methods stats graphics grDevices utils datasets base
581
582 other attached packages:
583
584 [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
585
586 loaded via a namespace (and not attached):
587
588 [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
589
590
591 </pre>
592
593 <div class="toolFormTitle">All output files available for downloading</div>
594
595 <div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
596
597 <tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.5 KB</td></tr>
598 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_MA_plot.pdf">DESeq2_edgeRtest_MA_plot.pdf</a></td><td>15.0 KB</td></tr>
599 <tr><td><a href="DESeq2_edgeRtest_PCA_plot.pdf">DESeq2_edgeRtest_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
600 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf">DESeq2_edgeRtest_dispersion_estimates.pdf</a></td><td>190.6 KB</td></tr>
601 <tr><td><a href="DESeq2_edgeRtest_qqplot.pdf">DESeq2_edgeRtest_qqplot.pdf</a></td><td>13.3 KB</td></tr>
602 <tr class="odd_row"><td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf">DESeq2_edgeRtest_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>
603 <tr><td><a href="Differential.log">Differential.log</a></td><td>1.4 KB</td></tr>
604 <tr class="odd_row"><td><a href="Differential_Counts.Rscript">Differential_Counts.Rscript</a></td><td>28.3 KB</td></tr>
605 <tr><td><a href="Differential_Counts_error.log">Differential_Counts_error.log</a></td><td>1.8 KB</td></tr>
606 <tr class="odd_row"><td><a href="Differential_Counts_runner.log">Differential_Counts_runner.log</a></td><td>1.3 KB</td></tr>
607 <tr><td><a href="Differential_rowsum_bar_charts.pdf">Differential_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>
608 <tr class="odd_row"><td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf">Differential_venn_edgeRtest_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>
609 <tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>
610 <tr class="odd_row"><td><a href="VOOM_edgeRtest_mean_variance_plot.pdf">VOOM_edgeRtest_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>
611 <tr><td><a href="VOOM_edgeRtest_qqplot.pdf">VOOM_edgeRtest_qqplot.pdf</a></td><td>17.5 KB</td></tr>
612 <tr class="odd_row"><td><a href="edgeR.log">edgeR.log</a></td><td>10.4 KB</td></tr>
613 <tr><td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf">edgeR_edgeRtest_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
614 <tr class="odd_row"><td><a href="edgeR_edgeRtest_GoodnessofFit.pdf">edgeR_edgeRtest_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
615 <tr><td><a href="edgeR_edgeRtest_MDSplot.pdf">edgeR_edgeRtest_MDSplot.pdf</a></td><td>4.9 KB</td></tr>
616 <tr class="odd_row"><td><a href="edgeR_edgeRtest_qqplot.pdf">edgeR_edgeRtest_qqplot.pdf</a></td><td>15.2 KB</td></tr>
617 <tr><td><a href="edgeR_edgeRtest_smearplot.pdf">edgeR_edgeRtest_smearplot.pdf</a></td><td>16.7 KB</td></tr>
618 <tr class="odd_row"><td><a href="edgeR_edgeRtest_top_100_heatmap.pdf">edgeR_edgeRtest_top_100_heatmap.pdf</a></td><td>11.2 KB</td></tr>
619 </table></div><br/>
620 </div></body></html>
621