Multiple Contrasts

Multiple contrasts

All pairwise contrasts

Run all pairs (current method) computes every pairwise contrast with the current method and thresholds. FDR is controlled within each contrast; no joint model across contrasts is fitted.

Outputs:

• A summary table of up and down hits per contrast.
• An UpSet plot of hit-set intersections. Click a bar for its genes.
• A volcano grid with one panel per contrast.

Venn diagrams

Select two or three contrasts and a direction (either, up only, down only). Region counts are exact set partitions. Circle areas are not proportional to counts, because exact area-proportional three-set diagrams are generally impossible; the plot states this. Click a region to list its genes; Export regions CSV writes every gene with its membership pattern.

Comparing two contrasts

Compare two contrasts plots the log₂FC of one contrast against another, with a regression line, and lists genes shared by both contrasts or exclusive to one.

Enrichment across contrasts

See Gene-set testing.

Any-group test

For the question "does this gene differ among any groups", use the genome-wide moderated F test (Group Patterns tab), which uses all samples in a single test rather than many pairwise tests.