[BioC] difference in RMA

[Marco Fabbri]

Christian,
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.

thank you

Marco
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
> normalization.
>
> Regards
> Christian
> _._._._._._._._._._._._._._._._
> 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
> >>
> >
> >
>
>


-- 
---------------------------------------
Marco Fabbri
Istituto Clinico Humanitas
via Manzoni, 56
20089 Rozzano (Mi)
Tel. 028224 5130
Fax 028224 5101