[BioC] unknown error in DiffBind package
Roberta Sanfilippo [guest]
guest at bioconductor.org
Mon Apr 14 18:41:52 CEST 2014
Hello!
I am using the DiffBind package to search for differences in histone modifications of ChIPseq peak data, I created a .csv files using sorted.bam files as both bamReads and Bamcontrol and bed files as Peaks column. I tried to count reads using the dba.count function and changing the value minOverlap from 0 to 4, but every time I obtained:
Error in if (res[i] == -1) { : missing value where TRUE/FALSE needed
WOuld you help me please?
thank you
Roberta
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] DiffBind_1.8.4 GenomicRanges_1.14.4 XVector_0.2.0
[4] IRanges_1.20.7 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] amap_0.8-12 bitops_1.0-6 caTools_1.16 edgeR_3.4.2
[5] gdata_2.13.2 gplots_2.12.1 gtools_3.3.1 KernSmooth_2.23-10
[9] limma_3.18.9 RColorBrewer_1.0-5 stats4_3.0.2 tools_3.0.2
[13] zlibbioc_1.8.0
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