DiffBind error loading dba
0
0
Entering edit mode
Rory Stark ★ 4.5k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK
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 >> >
GO DiffBind NarrowPeaks GO DiffBind NarrowPeaks • 747 views
ADD COMMENT

Login before adding your answer.

Traffic: 335 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6