[BioC] DiffBind -error with dba.counts

[Gordon Brown]

Hi, Anitha,

The basic problem is that you have two samples, but you're asking for a
minOverlap of 3 (i.e. for peaks which occur in at least 3 samples).  No
locations can satisfy that criterion, so you end up with an empty set of
peaks.

The message is obscure, I will admit.  (It happens because DiffBind writes
out the unified set of peaks and reads it back in, for tedious
implementation reasons, and when it reads it back in, there are no peaks,
hence "no lines available in input".)

Try using minOverlap=2.   But... having said that, I'm not sure how useful
DiffBind will be to you, without replicates.

Cheers,

 - Gord Brown



>Message: 22
>Date: Fri, 13 Sep 2013 12:21:02 -0600
>From: Anitha Sundararajan <asundara at ncgr.org>
>To: bioconductor at r-project.org
>Subject: [BioC] DiffBind -error with dba.counts
>Message-ID: <5233578E.3090701 at ncgr.org>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Hi
>
>I have been trying to use DiffBind to analyze our Chip-seq data and have
>been running into some errors repeatedly.
>
>I first created a samplesheet.csv describing my samples and it looks
>like this:
>
>SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,PeakC
>aller 
>
>meio.1,meiocytes,H3K4me3,N,1,M_meiocytes_H3K4me3.bam,InM_input_meiocytes.b
>am,meio.vs.in.rep1.def_peaks.bed,MACS
>
>seed.1,seedlings,H3K4me3,N,1,S_seedling_H3K4me3.bam,InS_input_seedling.bam
>,seed.vs.in.rep1.def_peaks.bed,MACS
>
>
>I only have two samples (and their respective inputs) with one rep each
>and the peaks were called using MACS v2. The peak caller generated .bed
>files which was used in DiffBind.
>
>
>I defined the working directory in R first.
>
>I then read the sample sheet in :
> > H3K4.B73=dba(sampleSheet='samplesheet2.csv',peakFormat='bed')
>
> >H3K4.B73
>
>2 Samples, 38870 sites in matrix (45304 total):
>       ID    Tissue  Factor Condition Replicate Peak.caller Intervals
>1 meio.1 meiocytes H3K4me3        N         1        MACS     44124
>2 seed.1 seedlings H3K4me3         N         1        MACS     41596
>
>generated a plot,
> > plot(H3K4.B73)
>
>And then when I tried to perform dba.counts, it continuously fails on
>me.  I went through the thread to find similar posts and could not find
>a solution.  I tried the floowing command:
>
> > H3K4.B73=dba.count(H3K4.B73, minOverlap=3)
>and this,
> > H3K4.B73=dba.count(H3K4.B73, minOverlap=3, bLowMem=TRUE)
> > H3K4.B73=dba.count(H3K4.B73, minOverlap=3, bLowMem=FALSE)
>And they all failed.
>
>My error in all three cases is as follows:
>Error in read.table(fn, skip = skipnum) : no lines available in input
>
>Please let me know if you have any insights on it.
>
>Thanks so much for your help in advance.
>
>Anitha Sundararajan Ph.D.
>Research Scientist
>National Center for Genome Resources
>Santa Fe, NM 87505