Question: difference in RMA
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gravatar for marco fabbri
11.5 years ago by
marco fabbri320
Italy
marco fabbri320 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
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ADD COMMENTlink modified 11.5 years ago by Williams, Alan40 • written 11.5 years ago by marco fabbri320
Answer: difference in RMA
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gravatar for James W. MacDonald
11.5 years ago by
United States
James W. MacDonald50k 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 -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENTlink written 11.5 years ago by James W. MacDonald50k
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 >> > >
ADD REPLYlink written 11.5 years ago by cstrato3.9k
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
ADD REPLYlink written 11.5 years ago by marco fabbri320
Answer: difference in RMA
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gravatar for Williams, Alan
11.5 years ago by
Williams, Alan40 wrote:
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ADD COMMENTlink written 11.5 years ago by Williams, Alan40
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