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:

Up Flat Down
Day 0-Day 14 376 682 35

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

    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