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1 <html>
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2 <head>
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3 <title>EdgeR Output</title>
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4 </head>
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5 <body>
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6 <h3>EdgeR Analysis Output:</h3>
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7 <h4>Input Summary:</h4>
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8 <ul>
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9 <li>Number of Samples: 4</li>
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10 <li>Number of Hairpins: 1105</li>
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11 <li>Number of annotations provided: 1105</li>
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12 <li>Number of annotations matched to hairpin: 1105</li>
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13 </ul>
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14 The estimated common biological coefficient of variation (BCV) is: 0.9323<br />
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15 No secondary factor specified.<br />
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16 <h4>Output:</h4>
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17 PDF copies of JPEGS available in 'Plots' section.<br />
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18 <img src="barIndex.png" alt="Counts per Index" height="600" width="600"/>
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19 <img src="barHairpin.png" alt="Counts per Hairpin" height="600" width="600"/>
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20 <img src="mds.png" alt="MDS Plot" height="600" width="600"/>
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21 <img src="bcv.png" alt="BCV Plot" height="600" width="600"/>
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22 <img src="smear(Day.0-Day.14).png" alt="Smear Plot(Day.0-Day.14)" height="600" width="600"/>
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23 <br />
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24 <h4>Differential Representation Counts:</h4>
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25 <table border="1" cellpadding="4">
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26 <tr>
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27 <td></td>
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28 <th>Up</th>
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29 <th>Flat</th>
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30 <th>Down</th>
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31 </tr>
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32 <tr>
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33 <th>Day 0-Day 14</th>
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34 <td>376</td>
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35 <td>682</td>
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36 <td>35</td>
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37 </tr>
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38 </table><h4>Plots:</h4>
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39 <a href="barIndex.pdf" target="_blank">Counts per Index Barplot (.pdf)</a><br />
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40 <a href="barHairpin.pdf" target="_blank">Counts per Hairpin Barplot (.pdf)</a><br />
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41 <a href="mds.pdf" target="_blank">MDS Plot (.pdf)</a><br />
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42 <a href="bcv.pdf" target="_blank">BCV Plot (.pdf)</a><br />
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43 <a href="smear(Day.0-Day.14).pdf" target="_blank">Smear Plot(Day.0-Day.14) (.pdf)</a><br />
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44 <h4>Tables:</h4>
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45 <a href="toptag(Day.0-Day.14).tsv" target="_blank">Top Tags Table(Day.0-Day.14) (.tsv)</a><br />
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46 <a href="counts.tsv" target="_blank">Counts table (.tsv)</a><br />
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47 <p>Alt-click links to download file.</p>
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48 <p>Click floppy disc icon on associated history item to download all files.</p>
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49 <p>.tsv files can be viewed in Excel or any spreadsheet program.</p>
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50 <h4>Additional Information:</h4>
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51 <li>Data was gathered from a table of counts.</li>
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52 <li>Target sequences without more than 0.5 CPM in at least 1 samples are insignificant and filtered out.</li>
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53 <li>1 of 1094 (0.09%) target sequences were filtered out for low count-per-million.</li>
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54 <li>Samples that did not produce more than 1000 counts were filtered out.</li>
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55 <li>0 samples were filtered out for low counts.</li>
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56 <li>An exact test was performed on each target sequence.</li>
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57 <h4>Citations</h4><ol>
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58 <li>Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140</li>
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59 <li>Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887</li>
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60 <li>Robinson MD and Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332</li>
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61 <li>McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40, 4288-4297</li>
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62 </ol>
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63 <p>Report problems to: su.s@wehi.edu.au</p>
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64 <a href="session_info.txt" target="_blank">Session Info</a><br />
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65 <table border="0">
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66 <tr>
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67 <td>Task started at:</td>
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68 <td>2015-01-20 12:16:59</td>
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69 </tr>
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70 <tr>
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71 <td>Task ended at:</td>
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72 <td>2015-01-20 12:17:05</td>
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73 </tr>
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74 <tr>
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75 <td>Task run time:</td>
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76 <td>6 secs</td>
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77 <tr>
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78 </table>
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79 </body>
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80 </html> |
