Hi all,

I am trying to use DiffBind to compare peaks called in control vs
condition. I have 2 replicates for each and I've also called peaks using 2
different peak callers (to wi, MACS and QuEST). I've also prepared a sample
data sheet that looks like this:
SampleID   Tissue   Factor   Condition   Replicate  Peak.caller  bamReads
bamControl   Peaks
control         Hela      TF              wt              1
MACS          path             path                path
control         Hela      TF              wt              1
QuEST         path             path                path
control2       Hela      TF            wt              2
MACS          path             path                path
control 2      Hela      TF            wt              2
QuEST         path             path                path
(and the same for the conditions)

My plan was to load all the data and then using diffbind selecte a set of
common peaks for the peak callers before proceeding with the analysis.
However, when I load the data (data = dba(sampleSheet="samplesheet.csv"))
the peaks for each caller are not recognized as a different variable.  How
I can do that and is this silly?

I could also derive a set of common peaks independently but it would be
neat to do it all with the same package and that seems to be possible but I
could not find how to do it in the documentation.

Thanks,
António


-- 
-- 
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domingue@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

	[[alternative HTML version deleted]]

