Mercurial > repos > fubar > shrnaseq_test

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<title>EdgeR Output</title>
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<h3>EdgeR Analysis Output:</h3>
<h4>Input Summary:</h4>
<ul>
<li>Number of Samples: 4</li>
<li>Number of Hairpins: 1105</li>
<li>Number of annotations provided: 1105</li>
<li>Number of annotations matched to hairpin: 1105</li>
</ul>
The estimated common biological coefficient of variation (BCV) is: 0.9323<br />
No secondary factor specified.<br />
<h4>Output:</h4>
PDF copies of JPEGS available in 'Plots' section.<br />
<img src="barIndex.png" alt="Counts per Index" height="600" width="600"/>
<img src="barHairpin.png" alt="Counts per Hairpin" height="600" width="600"/>
<img src="mds.png" alt="MDS Plot" height="600" width="600"/>
<img src="bcv.png" alt="BCV Plot" height="600" width="600"/>
<img src="smear(Day.0-Day.14).png" alt="Smear Plot(Day.0-Day.14)" height="600" width="600"/>
<br />
<h4>Differential Representation Counts:</h4>
<table border="1" cellpadding="4">
<tr>
<td></td>
<th>Up</th>
<th>Flat</th>
<th>Down</th>
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<th>Day 0-Day 14</th>
<td>376</td>
<td>682</td>
<td>35</td>
</tr>
</table><h4>Plots:</h4>
<a href="barIndex.pdf" target="_blank">Counts per Index Barplot (.pdf)</a><br />
<a href="barHairpin.pdf" target="_blank">Counts per Hairpin Barplot (.pdf)</a><br />
<a href="mds.pdf" target="_blank">MDS Plot (.pdf)</a><br />
<a href="bcv.pdf" target="_blank">BCV Plot (.pdf)</a><br />
<a href="smear(Day.0-Day.14).pdf" target="_blank">Smear Plot(Day.0-Day.14) (.pdf)</a><br />
<h4>Tables:</h4>
<a href="toptag(Day.0-Day.14).tsv" target="_blank">Top Tags Table(Day.0-Day.14) (.tsv)</a><br />
<a href="counts.tsv" target="_blank">Counts table (.tsv)</a><br />
<p>Alt-click links to download file.</p>
<p>Click floppy disc icon on associated history item to download all files.</p>
<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>
<h4>Additional Information:</h4>
<li>Data was gathered from a table of counts.</li>
<li>Target sequences without more than 0.5 CPM in at least 1 samples are insignificant and filtered out.</li>
<li>1 of 1094 (0.09%) target sequences were filtered out for low count-per-million.</li>
<li>Samples that did not produce more than 1000 counts were filtered out.</li>
<li>0 samples were filtered out for low counts.</li>
<li>An exact test was performed on each target sequence.</li>
<h4>Citations</h4><ol>
<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>
<li>Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887</li>
<li>Robinson MD and Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332</li>
<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>
</ol>
<p>Report problems to: su.s@wehi.edu.au</p>
<a href="session_info.txt" target="_blank">Session Info</a><br />
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<td>Task started at:</td>
<td>2015-01-20 12:16:59</td>
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<td>Task ended at:</td>
<td>2015-01-20 12:17:05</td>
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<td>Task run time:</td>
<td>6 secs</td>
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author	fubar
date	Mon, 19 Jan 2015 22:11:00 -0500
parents	17a83efb37f9
children