[BioC] DiffBind error loading dba

[Rory Stark]

On 12/02/2014 11:34, "Gordon Brown" <Gordon.Brown at cruk.cam.ac.uk> wrote:

>Hi, Sharona,
>
>Part of the problem is that some of your peaks have width zero (or 1,
>depending on the exact definition of "narrow" format).  For example, line
>12826 of synch_PolII_rep1_narrowPeakn.bed is
>
>---------------
>chr1	84765176	84765176	.	9.263	.	9.263	1.709270e+00	2.493753e-02	0
>---------------
>
>When DiffBind tries to normalise the score based on the width of the peak,
>it comes out as N/0, which R shows as infinity.  Things go downhill from
>there.  This is a bug in DiffBind (if the width is zero, we should just
>make it 1, for example).  But in the meantime, to work around it, just
>remove those peaks (or add 1 to the right coordinate).  (In bed format,
>intervals are represented as half-open, i.e. the right end is one past the
>end of the interval; I'll have to check the exact definition of "narrow"
>format to see if we should be interpreting the coordinates differently.)
>
>Regarding memory usage, the latest version of DiffBind is *much* more
>memory efficient than previous ones, so upgrading should take care of
>that.
>
>Cheers,
>
> - Gord
>
>
>On 2014-02-11 18:10, "Sharona Elgavish" <SharonaE at ekmd.huji.ac.il> wrote:
>
>>Dear all,
>>
>>I'm trying to upload my Chip-Seq data to DiffBind and receive the
>>following error:
>>
>>>  pol = dba(sampleSheet="pol_narrow_bam_allpeaks.csv",
>>>peakFormat="narrow")
>>
>>polsyn1 hella pol synchronized  1 narrow
>>polsyn2 hella pol synchronized  2 narrow
>>polunsyn1 hella pol unsynchronized  1 narrow
>>polunsyn2 hella pol unsynchronized  2 narrow
>>Error in if (res >= minval) { : missing value where TRUE/FALSE needed
>>
>>> sessionInfo()
>>R version 3.0.1 (2013-05-16)
>>Platform: x86_64-pc-linux-gnu (64-bit)
>>
>>locale:
>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=C                 LC_NAME=C
>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>>attached base packages:
>>[1] parallel  stats     graphics  grDevices utils     datasets  methods
>>[8] base
>>
>>other attached packages:
>>[1] DiffBind_1.6.2       Biobase_2.20.1       GenomicRanges_1.12.5
>>[4] IRanges_1.18.4       BiocGenerics_0.6.0   BiocInstaller_1.10.4
>>
>>loaded via a namespace (and not attached):
>> [1] amap_0.8-7         bitops_1.0-6       caTools_1.16       edgeR_3.2.4
>> [5] gdata_2.13.2       gplots_2.12.1      gtools_3.2.1
>>KernSmooth_2.23-10
>> [9] limma_3.16.8       RColorBrewer_1.0-5 stats4_3.0.1       tools_3.0.1
>>
>>[13] zlibbioc_1.6.0
>>
>>
>>
>>I get that error message whether I install DiffBind through the
>>Bioconductor that is, biocLite("DiffBind"), or by installing
>>DiffBind_1.8.3 by
>>install.packages(DiffBind_1.8.3.tar.gz")
>>
>>When I took only the first 4000 peaks in each of the peak files (I have
>>4) I easily manged to upload the dba. However, running dba.count was
>>successful only upon using the bUseSummarizeOverlaps=TRUE,
>>bParallel=FALSE options
>>
>>The peak files are in narrowPeaks format and were generated using the
>>program PeakSeq.
>>
>>The peak files contain 10,000-32,000 peaks
>>
>>Am I out of memory? In case I am, how can I increase the memory during
>>the upload (and not at dba.count)?
>>
>>I attached the sampleSheet and the 4 peaks files.
>>
>>
>>I would much appreciate any help
>>Thanks!
>>
>>Sharona
>>
>