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Volcano Plot

Purpose:

  • inspect differential expression for a selected contrast
  • prioritize strongly changing and significant features

Inputs:

  • one loaded dataset with processed output
  • selected contrast
  • p-value cutoff
  • LFC cutoff
  • optional feature highlight search

How to use:

  1. Open Volcano Plot.
  2. Choose contrast.
  3. Set p-value and LFC cutoffs.
  4. Optionally search/highlight features.
  5. Click compute.

Outputs:

  • interactive volcano plot
  • significant-feature table for export

Interpretation tips:

  • Upper-left / upper-right regions typically capture strong regulated features.
  • Check that highlighted candidates behave as expected under chosen contrast.
  • Use same thresholds when comparing across runs.

Volcano Plot after compute

Figure 3. Volcano Plot after compute. Each point is a feature in the selected contrast; the x-axis shows log2 fold change and the y-axis shows statistical evidence as -log10(p-value). Dashed lines mark the selected LFC and p-value cutoffs.

Help: how to read this plot

Features farther left or right have larger effect sizes, and features higher on the plot have stronger statistical evidence. Points in the upper-left and upper-right regions are usually the most interesting candidates. Gray points do not pass the selected thresholds, while colored points pass the significance and direction criteria.