[BioC] difference in RMA
fabbri.marco at gmail.com
Sat Feb 9 07:52:43 CET 2008
thnk you for your rpaly but I do not think this is the problem because
when I use the human plus 2.0 chip, there are no difference, I think
the that it is something related to the gene chip.
On 09/02/2008, cstrato <cstrato at aon.at> wrote:
> Dear Marco
> I believe, the difference is that Partek does quantile normalization as
> in bioC package affy, but Expression Console does only sketch quantile
> C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
> V.i.e.n.n.a A.u.s.t.r.i.a
> James MacDonald wrote:
> > I would suggest you contact either Affy, GeneSpring or Partek.
> > Best,
> > Jim
> > Marco Fabbri wrote:
> >> Dear All,
> >> I am using the mouse gene 1.0 ST affymetrix. In order to run RMA I
> >> used expressionist console from affymetrix, genesping and partek.
> >> Genespring and partek give very similar results, instead expressionist
> >> console produce much higher difference between samples.
> >> I tried to understand more but there is little information around. Any
> >> suggestion?
> >> Thank you
> >> Marco
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