[BioC] dba.counts error
Ravi Karra
ravi.karra at gmail.com
Tue Jun 10 18:48:44 CEST 2014
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
>
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