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.