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.