[BioC] limma-voom and y$E

[Gordon K Smyth]

Dear Davide,

It is better to read the documentation for voom instead of trying to 
interpret the code.  You would then see that the default normalization is 
"normalization.method=none".

In fact, voom uses the normalization factors computed by edgeR and placed 
in the DGEList object to compute effective library sizes, so by default 
voom's normalization is exactly as for edgeR.

Best wishes
Gordon

> Date: Tue, 5 Feb 2013 07:07:51 +0100
> From: Davide Cittaro <cittaro.davide at hsr.it>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] limma-voom and y$E
>
> Hi all,
>
> Although limma-voom seems to give us really good results in our RNA-seq 
> experiments, we still have some doubt about y$E values (i.e. expression 
> values after voom). looking at function implementation it seems that 
> voom performs quantile normalization using normalizeBetweenArrays 
> function (default option). I need a clarification here: it has been 
> explained many times that limma (and edgeR too) do not need to take into 
> account gene length as they perform gene-wise statistical tests: feature 
> length does not change and so it is good to take into account library 
> size. It has also been explained that this method is good for DGE but 
> does not necessarily works for "absolute quantification" of a 
> transcript. But. AFAIK (but I may be wrong) quantile normalization works 
> by considering all features in each expression quantile together; in the 
> same quantile there could be low expressed long genes and highly 
> expressed short genes (if we only consider CPM), and I'm missing the 
> rationale behind. If the normalization process is correct I should be 
> able to use y$E values as "absolute" quantification (or absolute-like) 
> of a transcript. If the y$E cannot be used as absolute quantification, 
> is quantile normalization the proper way to do this?
>
> Sorry for the confused mail, it's early morning and I really need some 
> sleep...
>
> Thanks
>
> d
>

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