[BioC] Compare results from different analysis (Affymetrix)

Darlene Goldstein Darlene.Goldstein at epfl.ch
Wed Dec 13 23:40:37 CET 2006

Sean Davis <sdavis2 at ...> writes:

> On Wednesday 13 December 2006 02:56, Ingrid H. G. Østensen wrote:
> > Hi
> >
> > I usually do a quality control of the data before I turn the data set into
> > an ExpressionSet. If I use justRMA, how can I then quality control the data
> > to see if any array should be removed? Will it not be difficult if all the
> > arrays are corrected as they are read into the program?
> I don't know what you mean by quality control (specifically), but for many of 
> the quality-control measures, they are done independently on each chip, so 
> you could still load in batches to do your QC.  
> Sean

The package affyPLM uses a multichip approach to quality assessment.  To avoid
having to do this in batches, you might try the web-based interface RACE,
available at http://race.unil.ch

Best regards,


Darlene Goldstein
École Polytechnique Fédérale de Lausanne (EPFL)
Institut de mathématiques
Bâtiment MA, Station 8        Tel: +41 21 693 5565 
CH-1015 Lausanne              Fax: +41 21 693 4303

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