[BioC] Different Normalizations

Anja von Heydebreck heydebre at molgen.mpg.de
Sat Feb 7 19:12:39 MET 2004

Rafael A. Irizarry wrote:

>On Sat, 7 Feb 2004, Anja von Heydebreck wrote:
>>Hi Julia,
>>>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)
But the output of vsn is - at least approximately - on the natural log 

>exprs(eset) <- log2(exprs(eset))
Therefore, to obtain log2-values,  I would rather do

exprs(eset) <- log2(exp(exprs(eset))), or

exprs(eset) <- log2(exp(1))*exprs(eset)


Dr. Anja von Heydebreck                   
Max Planck Institute for Molecular Genetics  
Dept. Computational Molecular Biology
Ihnestr. 73
14195 Berlin, Germany                                   
heydebre at molgen.mpg.de             phone: +49-30-8413-1168
http://www.molgen.mpg.de/~heydebre   fax: +49-30-8413-1152

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