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

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Sat Apr 9 15:51:00 CEST 2005

Quoting Gordon K Smyth <smyth at wehi.EDU.AU>:

> 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.
> Gordon

bingo! :-)

thank you *soooo much* for a great and FAST reply...


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

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