[BioC] LimmaGUI discards spots with no signal on one channel?

[Ramon Diaz-Uriarte]

Thanks a lot for the answer, Gordon.

Best,

R.

On Monday 18 April 2005 13:33, Gordon K Smyth wrote:
> > Date: Mon, 18 Apr 2005 11:06:03 +0200
> > From: "Ramon Diaz-Uriarte" <rdiaz at cnio.es>
> > Subject: Re: [BioC] LimmaGUI discards spots with no signal on one
> >  channel?
> > To: <bioconductor at stat.math.ethz.ch>, <smyth at wehi.edu.au>
> > Cc: J.delasHeras at ed.ac.uk
> >
> >
> > Dear Gordon,
> >
> >> This is a characteristic of local background correction, it is not
> >> specifically a characteristic of limmaGUI.  It has everything to do with
> >> with the choice of image analysis program and background estimator that
> >> you're using.
> >>
> >> > How could I get around this?
> >>
> >> 1. Don't background correct, or
> >> 2. Use a background correction option which ensures positive corrected
> >> intensities, or 3. Switch to an image analysis program with a low stable
> >> background estimator available, e.g, SPOT or GenePix 6 with morph
> >> background.
> >>
> >> The authors of limma and limmaGUI always do 2. or 3. in their own work,
> >> because of the sort of problem that you mention.
> >
> > Is there any guidance (paper, tech. report,
>
> Not yet.
>
> > your experience)
>
> I currently use SPOT or GenePix 6 with morph background.  If I have to use
> local background, then I use normexp with a small offset.  There is an
> illustration of the effectness this in the Limma User's Guide.
>
> Gordon
>
> > on how to choose
> > among the options available in limma for backgroundCorrect that implement
> > 2. (i.e., half, minimum, edwards or normexp)?
> >
> >
> > Thanks,
> >
> > R.
> >
> >> Gordon
> >>
> >> > Jose
> >> >
> >> > --
> >> > Dr. Jose I. de las Heras                      Email:
> >> > J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology
> >> > Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology
> >> > Fax:   +44 (0)131 6507360 Swann Building, Mayfield Road
> >> > University of Edinburgh
> >> > Edinburgh EH9 3JR
> >> > UK

-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)




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