Hello, 

am wondering if it is possible to call the function dba.contrast without the controls files (i do not have them). I have created a DBA odject as follow:

mESC <- dba.peakset(NULL, bamReads = "/home/tandrean/Desktop/mESC/1.sorted.bam", bamControl = NULL,
                      peaks="/home/tandrean/Desktop/mESC/1.test_peaks.narrowPeak",
                      peak.caller="bed", peak.format= "narrow",
                      sampID="mESC.1",tissue="mESC",
                      factor="ER",condition="wt",replicate=1)
mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/2.sorted.bam",bamControl = NULL,
                      peaks="/home/tandrean/Desktop/mESC/2.test_peaks.narrowPeak",
                      peak.caller="bed", peak.format= "narrow",
                      sampID="mESC.2",tissue="mESC",
                      factor="ER",condition="wt",replicate=2)
mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/3.sorted.bam",bamControl = NULL,
                      peaks="/home/tandrean/Desktop/mESC/3.test_peaks.narrowPeak",
                      peak.caller="bed", peak.format= "narrow",
                      sampID="mESC.3",tissue="mESC",
                      factor="ER",condition="wt",replicate=3)

mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/4.sorted.bam",bamControl = NULL,
                    peaks="/home/tandrean/Desktop/Gadd45-TKO/4.test_peaks.narrowPeak",
                    peak.caller="bed", peak.format= "narrow",
                    sampID="Gadd45.TKO.1",tissue="mESC",
                    factor="ER",condition="TKO",replicate=1)
mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/5.sorted.bam",bamControl = NULL,
                    peaks="/home/tandrean/Desktop/Gadd45-TKO/5.test_peaks.narrowPeak",
                    peak.caller="bed", peak.format= "narrow",
                    sampID="Gadd45.TKO.2",tissue="mESC",
                    factor="ER",condition="TKO",replicate=2)
mESC <- dba.peakset(mESC, bamReads = "/home/tandrean/Desktop/mESC/6.sorted.bam",bamControl = NULL,
                    peaks="/home/tandrean/Desktop/Gadd45-TKO/6.test_peaks.narrowPeak",
                    peak.caller="bed", peak.format= "narrow",
                    sampID="Gadd45.TKO.3",tissue="mESC",
                    factor="ER",condition="TKO",replicate=3)

Object is like this:

6 Samples, 41954 sites in matrix (59633 total):
            ID Tissue Factor Condition Replicate Caller Intervals
1       mESC.1   mESC     ER        wt         1    bed     33689
2       mESC.2   mESC     ER        wt         2    bed     32901
3       mESC.3   mESC     ER        wt         3    bed     34305
4 Gadd45.TKO.1   mESC     ER       TKO         1    bed     40043
5 Gadd45.TKO.2   mESC     ER       TKO         2    bed     40913
6 Gadd45.TKO.3   mESC     ER       TKO         3    bed     40377

and run the dba.contrast function:

mESC <- dba.contrast(mESC, categories = DBA_CONDITION)

and it returns:

Warning message:
Model must include count data for contrasts. 

traceback() 
1: dba.analyze(mESC, categories = condition)

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] DiffBind_2.0.9             SummarizedExperiment_1.2.3 Biobase_2.32.0             GenomicRanges_1.24.3      
[5] GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7             locfit_1.5-9.1          lattice_0.20-34         GO.db_3.3.0            
 [5] Rsamtools_1.24.0        Biostrings_2.40.2       gtools_3.5.0            assertthat_0.1         
 [9] digest_0.6.12           R6_2.2.0                plyr_1.8.4              BatchJobs_1.6          
[13] backports_1.0.5         ShortRead_1.30.0        RSQLite_1.1-2           ggplot2_2.2.1          
[17] gplots_3.0.1            zlibbioc_1.18.0         GenomicFeatures_1.24.5  lazyeval_0.2.0         
[21] annotate_1.50.1         gdata_2.17.0            Matrix_1.2-8            checkmate_1.8.2        
[25] systemPipeR_1.6.4       GOstats_2.38.1          splines_3.3.2           BiocParallel_1.6.6     
[29] stringr_1.1.0           pheatmap_1.0.8          RCurl_1.95-4.8          biomaRt_2.28.0         
[33] munsell_0.4.3           sendmailR_1.2-1         rtracklayer_1.32.2      base64enc_0.1-3        
[37] BBmisc_1.10             fail_1.3                tibble_1.2              edgeR_3.14.0           
[41] XML_3.98-1.5            AnnotationForge_1.14.2  dplyr_0.5.0             GenomicAlignments_1.8.4
[45] bitops_1.0-6            grid_3.3.2              RBGL_1.48.1             xtable_1.8-2           
[49] GSEABase_1.34.1         gtable_0.2.0            DBI_0.5-1               magrittr_1.5           
[53] scales_0.4.1            graph_1.50.0            KernSmooth_2.23-15      amap_0.8-14            
[57] stringi_1.1.2           XVector_0.12.1          hwriter_1.3.2           genefilter_1.54.2      
[61] limma_3.28.21           latticeExtra_0.6-28     brew_1.0-6              rjson_0.2.15           
[65] RColorBrewer_1.1-2      tools_3.3.2             Category_2.38.0         survival_2.40-1        
[69] AnnotationDbi_1.34.4    colorspace_1.3-2        caTools_1.17.1          memoise_1.0.0   

Does anyone has already experienced this problem?

Thanks in advance.

 Contrasts can only be set up using count data for a consensus peakset. You need to call dba.count() first, before calling dba.contrast() and/or dba.analyze().

Regards-

Rory