[BioC] DiffBind error

[Rory Stark]

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


On Tue, 29 Jan 2013 15:21:23 +0100, 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
>
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