[BioC] Different Normalizations

[Susan Holmes]

On Fri, 6 Feb 2004, Julia Engelmann wrote:

>
> 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?
>

Julia,
vsn doesn't use log (base) but a different trasnformation that stabilizes
the variance, I have found the results to be quite different too,
they are meant to be especially if there is a strong dependency between
variance and expression levels.

Best
Susan Holmes
Associate Professor
Statistics
Stanford