[BioC] DEseq for chip-seq data normalisation

Giuseppe Gallone giuseppe.gallone at dpag.ox.ac.uk
Wed Nov 6 11:48:56 CET 2013

Thanks a lot Rory. Do you think it would then make sense to use the 
normalised counts in the peaks to build a ratio based on the raw count 
and then feed this ratio to, say, picard to get a downsampled bam from 
the original bam?


On 11/05/13 18:18, Rory Stark wrote:
> Hi Guiseppe-
> You can retrieve the complete matrix of read counts from DiffBind, either
> normalized or not, using dba.peakset with bRetrieve=TRUE. To can set the
> score to use via dba.count with peaks=NULL and score=DBA_SCORE_READS, or
> any of the other possible score values. The default score is
> DBA_SCORE_TMM_MINUS_FULL, which is normalized using edgeR's TMM method,
> after subtracting the reads in the control, and using the full library
> size (not just the reads in peaks) as a scalar.
> Cheers-
> Rory

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