Question: DiffBind: same numbers in dba.overlap
0
gravatar for Udi Landau
3.8 years ago by
Udi Landau30
Udi Landau30 wrote:

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         

 

diffbind dba.overlap • 791 views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Udi Landau30

You should change your tag to diffbind so the author sees your question. Also show the output of sessionInfo().

Valerie

ADD REPLYlink written 3.8 years ago by Valerie Obenchain6.7k

Thanks Valerie. 

ADD REPLYlink written 3.8 years ago by Udi Landau30
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