Dear all,
I am trying to analyze ChIP-Seq data using DiffBind. After creating a CSV file with the experiment design and the peak files information. like shown in the DiffBind vignette, I used the following command to create a DBA object:
H3K27ac_samples.dba = dba( H3K27ac_samples )
However this gives me an error:
Error in matrix(defval, npeaks, numvecs + 3) :
invalid 'nrow' value (too large or NA)
A traceback() reveals:
4: matrix(defval, npeaks, numvecs + 3)
3: pv.vectors(model, mask = mask, minOverlap = minOverlap, bKeepAll = bKeepAll,
bAnalysis = bAnalysis, attributes = attributes)
2: pv.model(DBA, mask = mask, minOverlap = minOverlap, samplesheet = sampleSheet,
config = config, caller = peakCaller, format = peakFormat,
scorecol = scoreCol, bLowerBetter = bLowerScoreBetter, skipLines = skipLines,
bAddCallerConsensus = bAddCallerConsensus, bRemoveM = bRemoveM,
bRemoveRandom = bRemoveRandom, bKeepAll = TRUE, bAnalysis = TRUE,
attributes = attributes)
1: dba(H3K27ac_samples)
I am confused as to why this error is occurring. Any help is highly appreciated.
Thanking you.
sessionInfo() output:
R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-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=en_US.UTF-8 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_1.8.5 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_0.8-14 bitops_1.0-5 caTools_1.17 edgeR_3.4.2
[5] gdata_2.13.3 gplots_2.16.0 gtools_3.4.1 KernSmooth_2.23-10
[9] limma_3.18.13 RColorBrewer_1.0-5 stats4_3.0.2 zlibbioc_1.8.0
