Thanks Rory, I missed that requirement. Works perfectly now! Ravi On Jun 10, 2014, at 9:51 AM, Rory Stark <rory.stark at="" cruk.cam.ac.uk=""> wrote: > Hi Ravi- > > It looks like your sample sheet is missing the "bamReads" column, which > tells DiffBind where the bam files are that contain the aligned reads, so > dba.count doesn't know where to look for the reads to count! > > Cheers- > Rory > > On 10/06/2014 14:35, "Ravi Karra" <ravi.karra at="" gmail.com=""> wrote: > >> Hi, >> >> I am trying to use DiffBind to analyze my ChIP-Seq data. I used MACS2 as >> my peak caller and to adjust for input. I am able to use dba to load in >> the data and to generate a correlation heatmap using the MACS scores. >> >> However, I am unable to calculate a binding matrix based on affinity >> scores. When I use dba.count (), I get the follow error message: >> >> "Error in if (res[i] == -1) { : missing value where TRUE/FALSE needed" >> >> I am not really sure where the error is coming from and appreciate any >> help to troubleshoot. >> >> Thanks in advance, >> Ravi >> >> Code, traceback, and sessionInfo: >> >>> library (DiffBind) >>> >>> samples = read.csv ("~/Desktop/Data/Acetyl_sampleSheet.csv", header = T) >> Warning message: >> In read.table(file = file, header = header, sep = sep, quote = quote, : >> incomplete final line found by readTableHeader on >> '~/Desktop/Data/Acetyl_sampleSheet.csv' >>> samples >> SampleID Factor Condition Replicate >> 1 Ac_A1 K27Ac A 1 >> 2 Ac_A2 K27Ac A 2 >> 3 Ac_C1 K27Ac C 1 >> 4 Ac_C2 K27Ac C 2 >> Peaks >> 1 /Users/rk16/Desktop/Data/Ac_A1_input_adjusted_peaks.xls >> 2 /Users/rk16/Desktop/Data/Ac_A2_input_adjusted_peaks.xls >> 3 /Users/rk16/Desktop/Data/Ac_C1_input_adjusted_peaks.xls >> 4 /Users/rk16/Desktop/Data/Ac_C2_input_adjusted_peaks.xls >> PeakCaller >> 1 macs >> 2 macs >> 3 macs >> 4 macs >>> Ac = dba(sampleSheet = samples) >> Ac_A1 K27Ac A 1 macs >> Ac_A2 K27Ac A 2 macs >> Ac_C1 K27Ac C 1 macs >> Ac_C2 K27Ac C 2 macs >>> Ac = dba.count(Ac, minOverlap=2) >> Error in if (res[i] == -1) { : missing value where TRUE/FALSE needed >>> traceback () >> 3: pv.checkExists(todo) >> 2: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = >> score, >> bLog = bLog, insertLength = fragmentSize, bOnlyCounts = T, >> bCalledMasks = TRUE, minMaxval = filter, bParallel = bParallel, >> bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, >> bScaleControl = bScaleControl, >> filterFun = filterFun, bLowMem = bUseSummarizeOverlaps, readFormat >> = readFormat, >> summits = summits, minMappingQuality = mapQCth) >> 1: dba.count(Ac, minOverlap = 2) >>> sessionInfo () >> R version 3.1.0 (2014-04-10) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> 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] parallel stats graphics grDevices utils datasets >> [7] methods base >> >> other attached packages: >> [1] DiffBind_1.10.1 GenomicAlignments_1.0.1 >> [3] BSgenome_1.32.0 Rsamtools_1.16.0 >> [5] Biostrings_2.32.0 XVector_0.4.0 >> [7] limma_3.20.4 GenomicRanges_1.16.3 >> [9] GenomeInfoDb_1.0.2 IRanges_1.22.8 >> [11] BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] amap_0.8-12 BatchJobs_1.2 BBmisc_1.6 >> [4] BiocParallel_0.6.1 bitops_1.0-6 brew_1.0-6 >> [7] caTools_1.17 codetools_0.2-8 DBI_0.2-7 >> [10] digest_0.6.4 edgeR_3.6.2 fail_1.2 >> [13] foreach_1.4.2 gdata_2.13.3 gplots_2.13.0 >> [16] grid_3.1.0 gtools_3.4.1 iterators_1.0.7 >> [19] KernSmooth_2.23-12 lattice_0.20-29 plyr_1.8.1 >> [22] RColorBrewer_1.0-5 Rcpp_0.11.1 RSQLite_0.11.4 >> [25] sendmailR_1.1-2 stats4_3.1.0 stringr_0.6.2 >> [28] tools_3.1.0 zlibbioc_1.10.0 >