Hello,

I have two conditions with 2 and 3 biological replicates, I made a dba object like this:

k4 <- dba.count(k4, minOverlap = 2)

k4 <- dba.contrast(k4, categories = DBA_CONDITION, minMembers = 2)

k4 <- dba.analyze(k4, bSubControl = FALSE)

olap.rate <- dba.overlap(k4, mode = DBA_OLAP_RATE)

 olap.rate
[1] 17534 17534 17534 17534 17534

for some reason I get the same number of peaks for each replicate/treatment...

when I use plotVenn 

  dba.plotVenn(k4 ,k4$masks$Consensus & k4$masks$WT)

I get different numbers for each replicate.

Don't know if it matters but I have duplicated peaks in my BED file (with different scores).

Hope that Dr. Stark could help me with that...

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] DiffBind_1.16.3            RSQLite_1.0.0              DBI_0.3.1                 
 [4] locfit_1.5-9.1             GenomicAlignments_1.6.3    Rsamtools_1.22.0          
 [7] Biostrings_2.38.3          XVector_0.10.0             limma_3.26.7              
[10] SummarizedExperiment_1.0.2 Biobase_2.30.0             GenomicRanges_1.22.4      
[13] GenomeInfoDb_1.6.3         IRanges_2.4.6              S4Vectors_0.8.11          
[16] BiocGenerics_0.16.1        ggplot2_2.0.0             

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3             lattice_0.20-33         GO.db_3.2.2            
 [4] gtools_3.5.0            digest_0.6.9            plyr_1.8.3             
 [7] futile.options_1.0.0    BatchJobs_1.6           ShortRead_1.28.0       
[10] gplots_2.17.0           zlibbioc_1.16.0         GenomicFeatures_1.22.12
[13] annotate_1.48.0         gdata_2.17.0            Matrix_1.2-3           
[16] checkmate_1.7.0         systemPipeR_1.4.8       labeling_0.3           
[19] GOstats_2.36.0          splines_3.2.2           BiocParallel_1.4.3     
[22] stringr_1.0.0           pheatmap_1.0.8          RCurl_1.95-4.7         
[25] biomaRt_2.26.1          munsell_0.4.2           sendmailR_1.2-1        
[28] rtracklayer_1.30.1      base64enc_0.1-3         BBmisc_1.9             
[31] fail_1.3                edgeR_3.12.0            XML_3.98-1.3           
[34] AnnotationForge_1.12.2  bitops_1.0-6            grid_3.2.2             
[37] RBGL_1.46.0             xtable_1.8-0            GSEABase_1.32.0        
[40] gtable_0.1.2            magrittr_1.5            scales_0.3.0           
[43] graph_1.48.0            KernSmooth_2.23-15      amap_0.8-14            
[46] stringi_1.0-1           hwriter_1.3.2           genefilter_1.52.1      
[49] latticeExtra_0.6-26     futile.logger_1.4.1     brew_1.0-6             
[52] rjson_0.2.15            lambda.r_1.1.7          RColorBrewer_1.1-2     
[55] tools_3.2.2             Category_2.36.0         survival_2.38-3        
[58] AnnotationDbi_1.32.3    colorspace_1.2-6        caTools_1.17.1