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