[BioC] Diffbind error

[jluis.lavin at unavarra.es]

Dear list,

--I'm trying to use Diffbind package to analyze some samples from a ChIP
seq experiment.
--I created a .csv samplesheet with the following fields and which samples
to analyze:

SampleID Tissue	Factor	Condition Replicate Reads Control	Peaks

Chip_K27.1+ Neural K27 Responsive 1 Chip_K27.BED Input_K.BED  Chip_K27.BED

Chip_K27.2+ Neural K27 Responsive 1 Chip_K27d.BED Input_K.BED Chip_K27d.BED

--All my BED files have 6 lines and have been retrieved from MACS peak
caller.

--When Diffbind reads the sheet everything seems correct:

> chippy = dba(sampleSheet="Peaksets_sample_sheet.csv")

Chip_K27.1+ Neural K27 Responsive  1 raw
Chip_K27.2+ Neural K27 Responsive  1 raw

#it plots the correlation heatmap

> plot(chippy)

#But fails in this step after a while
> chippy = dba.count(chippy, minOverlap=3)

Error in read.table(fn, skip = skipnum) : no lines available in input

#Alternatively if I try this command
> chippy = dba.count(chippy)

Error in cond$counts : $ operator is invalid for atomic vectors
In addition: Warning message:
In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive =
TRUE) :
  all scheduled cores encountered errors in user code

Would any of you shed any light on this issue?

Best wishes and thanks in advance

JL


> sessionInfo()
R version 2.15.1 (2012-06-22)
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=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_1.4.0       Biobase_2.18.0       GenomicRanges_1.10.5
[4] IRanges_1.16.4       BiocGenerics_0.4.0   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
 [1] amap_0.8-7         edgeR_3.0.7        gdata_2.12.0       gplots_2.11.0
 [5] gtools_2.7.0       limma_3.14.3       RColorBrewer_1.0-5 stats4_2.15.1
 [9] tools_2.15.1       zlibbioc_1.4.0


-- 
Dr. José Luis Lavín Trueba

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN