Contrast Scatter — Compare Two Contrasts

Header: Contrast Scatter: Cross-Contrast Comparison

The Contrast Scatter report compares the fold changes of two contrasts directly. It merges the two result files on gene ID and plots each shared gene's log2FC in contrast A (x-axis) against its log2FC in contrast B (y-axis).

Reading the Plot

Genes are classified by how they behave in the two contrasts:

• Concordant — changed in the same direction in both (points along the diagonal).
• Discordant — changed in opposite directions (points on the opposite diagonal).
• One significant — significant in only one of the two contrasts.

Points far from the diagonal reveal condition-specific responses.

When to use it

Use Contrast Scatter to answer "do genes respond the same way to treatment A and treatment B?" — for comparing two treatments, two time points, or two tissues. For more than two contrasts at once, use Enrichment Compare or Upset.