[BioC] Different Normalizations

[Anja von Heydebreck]

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).

>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