[BioC] VSN combined with RMA
ririzarr at jhsph.edu
Mon Jul 19 23:16:43 CEST 2004
in principle it does not sound like a good idea since vsn does
something that could be considered bg correction.
in any case i have already seen the result of this and you get very
similar results to just using RMA (quantile normalization). look at the
RMAVSN entry in
On Jul 19, 2004, at 3:56 PM, Remo Sanges wrote:
> I' m planning to test vsn normalization on affymetrix arrays
> with RMA background correction.
> But from the vsn vignette and other messages in this list
> it seems to me that vsn on affymetrix chips is used without
> background correction:
> There is a reason for this?
> Is it wrong to use expresso in this way:
> d="pmonly",summary.method="medianpolish") ?
> Thank you
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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