Mercurial > repos > fubar > shrnaseq_test
diff test-data/shrnaseq_zuber_test.html @ 7:2c6bcbc1e76a draft default tip
Uploaded
| author | fubar |
|---|---|
| date | Mon, 19 Jan 2015 22:14:10 -0500 |
| parents | 17a83efb37f9 |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrnaseq_zuber_test.html Mon Jan 19 22:14:10 2015 -0500 @@ -0,0 +1,80 @@ +<html> +<head> +<title>EdgeR Output</title> +</head> +<body> +<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> +</tr> +<tr> +<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 /> +<table border="0"> +<tr> +<td>Task started at:</td> +<td>2015-01-20 12:16:59</td> +</tr> +<tr> +<td>Task ended at:</td> +<td>2015-01-20 12:17:05</td> +</tr> +<tr> +<td>Task run time:</td> +<td>6 secs</td> +<tr> +</table> +</body> +</html> \ No newline at end of file