[BioC] DEseq for chip-seq data normalisation

Ying Wu daiyingw at gmail.com
Wed Nov 6 20:08:16 CET 2013

Hi Rory,
Could you give some insight into why TMM is used with full library size, 
it seems to make sense for effective library size case but where full 
library size is used, would it still be valid to try and minimize 
changes between conditions?


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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