[BioC] DiffBind error

[Gordon Brown]

Hi,

Your sample sheet shows the same filename for "Reads" and "Peaks", which
is unlikely to be right.  The "Peaks" file should be the output of the
peak caller (the peaks that MACS called); the "Reads" file should be the
aligned reads, i.e. the *input* to the peak caller (the output of the
alignment stage).  Let me know if that fixes the problem.

It should give an informative error message, though... I'll add that to
the to-do list.

Cheers,

 - Gord


>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 19 Dec 2012 16:17:07 +0100
>From: jluis.lavin at unavarra.es
>To: bioconductor at r-project.org
>Subject: [BioC] Diffbind error
>Message-ID:
>	<e6a0d8855033e937b5236f5787e1d78d.squirrel at webmail.unavarra.es>
>Content-Type: text/plain;charset=iso-8859-1
>
>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. Jos? Luis Lav?n Trueba
>
>Dpto. de Producci?n Agraria
>Grupo de Gen?tica y Microbiolog?a
>Universidad P?blica de Navarra
>31006 Pamplona
>Navarra
>SPAIN