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Partek Flow Documentation

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When the task is selected, the dialog will display all the categorical attributes more than one subgroups (Figure 1).

 


Numbered figure captions
SubtitleTextCuffdiff setup dialog. “Select attributes(s) to groups samples” lists the categorical attributes which have at least two levels (e.g. “Cell type” and “Time”)
AnchorNameCuffdiff setup dialog.

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The report of the cuffdiff task is a table of a feature list p-values, q-value and log2 fold-change information for all the comparisons (Figure 20).

 


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SubtitleTextFigure 20: Cuffdiff task report. Each row is a feature, p-value, q-value and log2 fold change columns are display for each comparison
AnchorNameCuffdiff task report

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The table can be downloaded as a text file when clicking the Download button on the lower-right corner of the table.

References

  1. Benjamini, Y., Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing, JRSS, B, 57, 289-300.
  2. Storey JD. (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Annals of Statistics, 31: 2013-2035.
  3. Auer, 2011, A two-stage Poisson model for testing RNA-Seq
  4. Burnham, Anderson, 2010, Model selection and multimodel inference
  5. Law C, Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology, 2014 15:R29.
  6. http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#cuffdiff-output-files
  7. Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biology, 2010

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