[BioC] choosing normalization method for RNA-seq analysis

[Wolfgang Huber]

Fernando,

does it matter? I.e., for your data, do you get substantially different 
results from the different methods? If so, that might indicate a 
weakness of the data quality or of the experimental design that you 
would need to investigate in a manner specific to the dataset.

Unsurprisingly, my personal favorite is "RLE".

	Wolfgang

Biase, Fernando scripsit 17/03/11 22:53:
> Hi
>
> Working with edgeR package to analyze RNA-seq data, we have three
> options of normalization within calcNormFactors() function. Is there
> a way to test which one is more suitable for the data? If there is no
> test, is there a criteria to choose one over the other?
>
> Thanks in advance, Fernando
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber