• Manuals

Browse the manual

• Introduction to the Advanced RNA-Seq plugin
  • Input data and normalization
    • Normalization
    • Metadata
  • PCA for RNA-Seq
    • Principal component analysis plot (2D)
    • Principal component analysis plot (3D)
  • Differential Expression for RNA-Seq
    • The statistical model
    • Output of the Differential Expression for RNA-Seqtool
    • Statistical comparison tracks
    • The volcano plot
  • Create Heat Map for RNA-Seq
    • Clustering of features and samples
    • The heat map view
  • Create Expression Browser
    • The expression browser
  • Create Venn Diagram for RNA-Seq
    • Venn diagram table view
• Installation of the Advanced RNA-Seq plugin
• Uninstall
• Bibliography

Output of the Differential Expression for RNA-Seq tool

The Differential Expression for RNA-Seq tool produces different numbers and types of statistical comparison tracks depending on the settings of the Comparisons panel. Depending on the choice either a Wald test or a Likelihood Ratio test is used. For example, assume that we test a factor called `Tissue' with three groups: skin, liver, brain.

• Across groups (ANOVA-like) This mode tests for the effect of a factor across all groups.
  • Outputs produced: "Due to Tissue"
  • Test used: Likelihood ratio test
  • Fold change reports: The maximum pairwise fold change between any two of the three tissue types.
  • Max of group means reports: The maximum of the average group RPKM values among any of the tissue types for a gene.
• All group pairs tests for differences between all pairs of groups in a factor.
  • Outputs produced: "skin vs. liver", "skin vs. brain", "liver vs. brain"
  • Test used: Wald test
  • Fold change reports: The fold change in the defined order between the named pair of tissue types.
  • Max of group means reports: The maximum of the average group RPKM values between the two named tissue types.
• Against control group This mode tests for differences between all the groups in a factor and the named reference group. In this example the reference group is skin.
  • Outputs produced: "liver vs. skin", "brain vs. skin"
  • Test used: Wald test
  • Fold change reports: The fold change in the defined order between the named pair of tissue types.
  • Max of group means reports: The maximum of the average group RPKM values between the two named tissue types.

Note: Fold changes are calculated from the GLM, which corrects for differences in library size between the samples and the effects of confounding factors. It is therefore not possible to derive these fold changes from the original counts by simple algebraic calculations.

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