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

Ramon Diaz-Uriarte rdiaz at cnio.es
Mon Apr 18 11:06:03 CEST 2005

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, your experience) on how to choose 
among the options available in limma for backgroundCorrect that implement 2. 
(i.e., half, minimum, edwards or normexp)?



> 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
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

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

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