In the second Venn Diagram in the ChIPpeakAnno Vignette

## $vennCounts
##      peaks1 peaks2 Counts count.peaks1 count.peaks2
## [1,]      0      0     83            0            0
## [2,]      0      1      5            0            5
## [3,]      1      0      0            0            0
## [4,]      1      1     12           12           12

I do not understand the meaning of the first row, 0 0 83 , how could there be 83 peaks that do not exist in either set?

The counts 83 comes from totalTest - counts in overlaps or unique peaks=1e+2 - 12 - 5 = 83. Hope this help.