Hello Giuseppe-

There shouldn't be any problem not having control reads. This looks like it could a mismatch with the peak file format. Could you send me

  *   The mysamples.csv file
  *    The GM06986_peaks.bed.gz file (or just the first 100 lines or so)

I'll take a look and let you know what the problem is.

Cheers-
Rory

On 23/07/2013 17:11, "Giuseppe Gallone" <giuseppe.gallone@dpag.ox.ac.uk<mailto:giuseppe.gallone@dpag.ox.ac.uk>> wrote:

Dear Rory

I'm contacting you to know your thoughts on the possibility of using
DiffBind with a Chip-exo dataset. The dataset is composed of
transcription factor binding data for a large number of hapmap LCLs.

I have made a first attempt at utilising the program - I am however
experiencing some problems. I called peaks using MACS2 and also have raw
read data in .bed format. I tried to build an initial .csv file in the
following format

SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks,PeakCaller,PeakFormat,ScoreCol,LowerBetter
GM06986,,TF,stimulated,1,d_BED/TF_GM06986_reads.bed,,GM06986_peaks.bed.gz,MACS,raw,4,F

The bamControl field is empty, as is the Tissue field - The data is not
tissue specific, and as you might be aware chip-exo data does not
currently come with background/input control.

This is the command I use
tfr = dba(sampleSheet="mysamples.csv")


and this is the error:
Error in if (res >= minval) { : missing value where TRUE/FALSE needed
In addition: There were 30 warnings (use warnings() to see them)

with the generic warning being:
1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors

Is the error due to the lack of control reads? Thanks for your help &
suggestions.

Giuseppe


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