# HG changeset patch # User fubar # Date 1421723306 18000 # Node ID 17a83efb37f96f34453eefc096164d64c2317211 # Parent e7922416086d09bc1a5ced04aee9b739a967aa94 Uploaded diff -r e7922416086d -r 17a83efb37f9 test-data/shrnaseq_zuber_test.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shrnaseq_zuber_test.html Mon Jan 19 22:08:26 2015 -0500 @@ -0,0 +1,80 @@ + + +EdgeR Output + + +

EdgeR Analysis Output:

+

Input Summary:

+ +The estimated common biological coefficient of variation (BCV) is: 0.9323
+No secondary factor specified.
+

Output:

+PDF copies of JPEGS available in 'Plots' section.
+Counts per Index +Counts per Hairpin +MDS Plot +BCV Plot +Smear Plot(Day.0-Day.14) +
+

Differential Representation Counts:

+ + + + + + + + + + + + + +
UpFlatDown
Day 0-Day 1437668235

Plots:

+Counts per Index Barplot (.pdf)
+Counts per Hairpin Barplot (.pdf)
+MDS Plot (.pdf)
+BCV Plot (.pdf)
+Smear Plot(Day.0-Day.14) (.pdf)
+

Tables:

+Top Tags Table(Day.0-Day.14) (.tsv)
+Counts table (.tsv)
+

Alt-click links to download file.

+

Click floppy disc icon on associated history item to download all files.

+

.tsv files can be viewed in Excel or any spreadsheet program.

+

Additional Information:

+
  • Data was gathered from a table of counts.
    • +
  • Target sequences without more than 0.5 CPM in at least 1 samples are insignificant and filtered out.
    • +
  • 1 of 1094 (0.09%) target sequences were filtered out for low count-per-million.
    • +
  • Samples that did not produce more than 1000 counts were filtered out.
    • +
  • 0 samples were filtered out for low counts.
    • +
  • An exact test was performed on each target sequence.
    • +

    Citations

      +
    1. 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
      2. +
    2. Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23, 2881-2887
      3. +
    3. Robinson MD and Smyth GK (2008). Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics, 9, 321-332
      4. +
    4. 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
      5. +
    +

    Report problems to: su.s@wehi.edu.au

    +Session Info
    + + + + + + + + + + + + + +
    Task started at:2015-01-20 12:16:59
    Task ended at:2015-01-20 12:17:05
    Task run time:6 secs
    + + \ No newline at end of file