[BioC] Different Normalizations

[Julia Engelmann]

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);
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