Hello,

I have a question regarding the vennDiagram function in the limma package.

I'm trying to make a Venn Diagram comparing 3 groups relative to a control (4th group). I.e. group 1 vs group 4, group 2 vs group 4, group 3 vs group 4. My code is the following:

fit_contrast_venn <- contrasts.fit(fit_filter, contrast.matrix_v2)
efit_venn <- eBayes(fit_contrast_venn)
venn_results <- decideTests(efit_venn, adjust.method = "BH", adj.p.value = 0.05)
vennDiagram(venn_results, "include"="up")
vennDiagram(venn_results, "include"="down")

When I make the venn diagrams for up-regulated genes, am I making a Venn diagram for only the genes that are upregulated for all 3 groups (group 1, 2, and 3)? What happens to genes that are upregulated in group 1 but downregulated in group 2 or 3? WIll these also show up on the venn diagram?

I'm just trying to understand the Venn Diagram that I am producing.

Thank you,

When you use the include argument, you can interpret 'up' and 'down' to mean 'show me only those genes that are up or down-regulated'. So if you have a gene that is up in group 1 and down in groups 2 and 3, that gene will only appear in the unique section of the group 1 portion of the Venn diagram. if you say 'down', it will be in the intersection between groups 2 and 3, and if you say 'both' it will be in the central intersection between all groups.