jluis.lavin | 30 Jan 15:51 2013
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Re: DiffBind error

Hello again,

Thank you very much to Rory and Gordon for your kind and accurate help.
Changing the minMembers parameter everything seemed to work fine and I've
been able to perform the next steps of the whole analysis.

Now I'm struggling with the retrieval of the analysis data; when I try to
write the results into a .csv table with a simple command I get the
following error:

> write.csv( chippy, file="ChIPseq_diffbind.csv" )

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors =
stringsAsFactors) :
  cannot coerce class '"DBA"' into a data.frame

I read DiffBind's vignette and manual and I found the "save" command, but
it doesn't allow me to retrieve the data either.
Is there a way to coerce a DBA class object into a dataframe implemented
in DiffBind?
The person I'll be analyzing ChIPseq experiments for will need tables with
differentially bound sites from his data comparisons so I need to learn
how to get data out of DiffBind...

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] DESeq_1.10.1         lattice_0.20-10      locfit_1.5-8
[4] DiffBind_1.4.1       Biobase_2.18.0       GenomicRanges_1.10.5
[7] IRanges_1.16.4       BiocGenerics_0.4.0   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
 [1] amap_0.8-7           annotate_1.36.0      AnnotationDbi_1.20.3
 [4] DBI_0.2-5            edgeR_3.0.8          gdata_2.12.0
 [7] genefilter_1.40.0    geneplotter_1.36.0   gplots_2.11.0
[10] grid_2.15.1          gtools_2.7.0         KernSmooth_2.23-8
[13] limma_3.14.4         RColorBrewer_1.0-5   RSQLite_0.11.2
[16] splines_2.15.1       stats4_2.15.1        survival_2.36-14
[19] tools_2.15.1         XML_3.95-0.1         xtable_1.7-0
[22] zlibbioc_1.4.0

El Mie, 30 de Enero de 2013, 13:28, Rory Stark escribió:
>
> Hello-
>
> It looks like your sample sheet is fine.
>
> By default, if no contrasts are set up using dba.contrast,  when you call
> dba.analyze it attempts to add all the two-way contrasts between groups
> where there are at least three samples in each group. In your case,
> nothing meets these conditions, as there are only two "Resistant" samples.
>
> If you add a call to dba.contrast before the call to dba.analyze, you will
> get the contrast you desire:
>
>> chippy = dba.contrast(chippy, minMembers=2)
>
> or, slightly more explicitly:
>
>> chippy = dba.contrast(chippy, categories=DBA_CONDITION, minMembers=2)
>
> or, even more explicitly:
>
>> chippy = dba.contrast(chippy, group1=chippy$masks$Resistant, group2 =
>>chippy$masksResponsive, name1="Resistant", name2="Responsive")
>
> then:
>
>> chippy = dba.analyze(chippy)
>
> Cheers-
> Rory
>
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 Tue, 29 Jan 2013 15:21:23 +0100, jluis.lavin@... 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
>>
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>

--

-- 
Dr. José Luis Lavín Trueba

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

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