[BioC] DiffBind error

Wed Jan 30 12:17:35 CET 2013

Hi,

By default, dba.contrast won't create contrasts with less than 3 members
in each group.  The easiest solution is to set minMembers=2 when calling
dba.contrast:

> chippy = dba.contrast(chippy, categories=DBA_CONDITION, minMembers=2)

Or you can create the contrast explicitly:

> chippy = dba.contrast(chippy, group1=chippy$masks$Resistant,
>group2=chippy$masks$Responsive, name1="a name", name2="another name")

Hope this helps...

Cheers,

 - Gord

On 2013-01-29 14:21, "jluis.lavin at unavarra.es" <jluis.lavin at unavarra.es>
wrote:

>Dear list,
>
>I made a new samplesheet to use with DiffBind with this format:
>
>SampleID	Tissue	Factor	Condition	Replicate	bamReads	bamControl	Peaks
>Contrl1	Neural	K9	Resistant	1	Control1.bed	Contro_input.bed	Control1_peaks
>.bed
>Contrl2	Neural	K9	Resistant	2	Control2.bed	Control_input.bed	Control2_peak
>s.bed
>A4_1	Neural	K9	Responsive	1	A4_1.bed	A4_input.bed	A4_1_peaks.bed
>A4_2	Neural	K9	Responsive	2	A4_2.bed	A4_input.bed	A4_2_peaks.bed
>A21_1	Neural	K9	Responsive	1	A21_1.bed	A21_input.bed	A21_1_peaks.bed
>A21_2	Neural	K9	Responsive	2	A21_2.bed	A21_input.bed	A21_2_peaks.bed
>
>I can load the files,
>
>> chippy = dba(sampleSheet="Peaksets_sample_sheet.csv")
>
>plot them
>
>>plot(chippy)
>
>and count the reads,
>
>>chippy = dba.count(chippy, minOverlap=3)
>
>but when I try to establish a contrast based on the condition metadata, I
>get the following warning message:
>
>> chippy = dba.contrast(chippy, categories=DBA_CONDITION)
>
>Warning message:
>No contrasts added. Perhaps try more categories, or lower value for
>minMembers.
>
>So when I try to perform the analysis, it doesn't work:
>
>> chippy = dba.analyze(chippy)
>
>Error in pv.DBA(DBA, method, bSubControl, bFullLibrarySize, bTagwise =
>bTagwise,  :
>  Unable to perform analysis: no contrasts specified.
>In addition: Warning message:
>No contrasts added. Perhaps try more categories, or lower value for
>minMembers.
>
>->My questions are:
>-What is the contrast for DiffBind (I added the input for each set of
>samples, and 2 biological replicates as control)?
>-Is there something wrong with the sample sheet?
>-Shouldn't the files to analyze be in bed format?
>
>Thanks in advance
>
>JL
>
>
>El Jue, 20 de Diciembre de 2012, 14:36, jluis.lavin at unavarra.es escribió:
>> 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
>>
>>
>>
>
>
>-- 
>Dr. José Luis Lavín Trueba
>
>Dpto. de Producción Agraria
>Grupo de Genética y Microbiología
>Universidad Pública de Navarra
>31006 Pamplona
>Navarra
>SPAIN
>
>