Hello,

I am using the vennDiagram function from the limma library in R in order to understand the relationship of differentially expressed genes between my conditions. For a simple example, create a matrix:

m <- matrix(nrow=5, ncol=3, c(0, 1, 1, -1, 0, 1, 1, 1, 1, 0, -1, -1, -1, -1, -1))

Where the first column represents condition A, the second condition B, and the third C. The five rows represent five separate genes, and a positive 1 means the gene is up regulated in that condition, and a negative 1 means it is down regulated. (ETA: A 0 means the gene is not expressed in that condition.)

To create a Venn diagram showing which conditions share differentially expressed genes (not distinguishing up- or down-regulated genes):

vennDiagram(m, names=c("A", "B", "C"))

This shows that three genes are expressed in all three conditions, one is expressed by both B and C, and one is expressed only in C. From my understanding, the 0 in the corner means no genes are listed in the matrix that aren't expressed by any of the three conditions. (ETA: In other words, all five genes are expressed in at least one condition.)

To distinguish which genes are up and down regulated:

vennDiagram(m, names=c("A", "B", "C"), include=c("up", "down"))

I can understand how in this diagram, the numbers move because, for example, of the 3 genes differentially expressed by all three conditions, 2 were up regulated in A and B while down regulated in C. However, where is the 1 coming from in the corner? One gene is up-regulated but not expressed by any of the conditions? I haven't changed the matrix used to generate the diagrams, so all genes should be expressed by at least one of the conditions.

Any help is appreciated.

(ETA: The matrix looks like the following:)

         A    B     C
Gene1    0    1    -1
Gene2    1    1    -1
Gene3    1    1    -1
Gene4   -1    1    -1
Gene5    0    0    -1