[BioC] DiffBind error

[jluis.lavin at unavarra.es]

Thank you Gordon, it was my mistake, I missunderstood the sample sheet and
didn't create mine correctly.
I think the packege is very very useful and I can't wait to see it working
correctly with my samples  ;)

Best wishes

JL


El Jue, 20 de Diciembre de 2012, 12:17, Gordon Brown escribió:
> 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
>
>


-- 
Dr. José Luis Lavín Trueba

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