[BioC] Different Normalizations

[Rafael A. Irizarry]

On Sat, 7 Feb 2004, Anja von Heydebreck wrote:

> Hi Julia,
> 
> >Hi,
> >I am comparing different normalizations of Affymetrix microarrays:
> >1. expresso with rma, vsn, pmonly and medianpolish
> >2. calling rma and vsn with: eset=rma(Data); Set=vsn(eset);
> >
> rma gives you expression levels on the log scale, whereas
> vsn expects input values on the raw scale. So it doesn't make sense
> to call vsn after rma like in 2. (apart from the question why you
> should normalize your data twice - I guess in 1. you used rma only for
> background correction; but calling rma like in 2. involves also
> quantile normalization and medianpolish).

of cource you could do:

exprs(eset) <- 2^exprs(eset)
eset = vsn(eset)
exprs(eset) <- log2(exprs(eset))

this should make things look more alike.

> 
> >I know that medianpolish does log2 transformation and vsn does log 
> >transformation (base e), but when I compare the results, the difference 
> >between the two datasets is huge- not a matter of log-base.
> >Shouldn't the results be very similar?
> >
> >Any help would be much appreciated.
> >
> >Thanks,
> >Julia
> >  
> >
> Best,
> Anja
> 
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