[BioC] normalizing time course RNA-Seq data

AKSR anandksrao at gmail.com
Wed Dec 28 10:50:16 CET 2011


Hi all,

I have some RNA-Seq data:
4 reps per sample, 4 different genotypes & 9 time points
= 144 data points

I want to essentially know the best method to normalize across 
ALL time points  and for each INDIVIDUAL  genotype.
Is the state of the art normalization method today, TMM?
If yes, is TMM step-by-step procedure available any where?
(I do some Perl scripting, but I am pretty new to R)
I realize that edgeR might be using TMM for pair-wise 
comparison,  but I need to perform normalization across 
time points for each genotype. 


Irrespective of normalization strategy, will I have to choose
the base level sample aka reference for normalization?
Or can normalization be done independent of an 
overtly defined reference state? 
 - I know this is a naive question, sorry...
(If required, I would use time point zero as my reference state)

Thanks in advance for guiding me
AKSR



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