Marco,
 
The standard analysis method for the Gene arrays in Expression Console
uses sketch normalization and not the full quantile normalization; hence
the label "RMA-Sketch" in Expression Console. The older 3' IVT array
designs (like HG U133 Plus 2.0) have a default analysis method "3'
Expression Arrays - RMA" which does use the full quantile normalization.
So Christian's response is probably the reason for differences in EC.
Note that there may be other differences depending on the library files
used. Expression Console uses the PGF/CLF library files where as other
software packages may use the unsupported CDF file.
 
Best,
Alan
 
 
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> Date: Sat, 9 Feb 2008 07:52:43 +0100
> From: "Marco Fabbri" <fabbri.marco@gmail.com>
> Subject: Re: [BioC] difference in RMA
> To: cstrato <cstrato@aon.at>
> Cc: bioconductor@stat.math.ethz.ch
> Message-ID:
> <3d25277f0802082252o1b00b96fxebf208354ac60a0@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> 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@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.
> >
> >
> > >
> > >> 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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