[BioC] LimmaGUI discards spots with no signal on one channel?
Gordon K Smyth
smyth at wehi.EDU.AU
Mon Apr 18 13:33:09 CEST 2005
> 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
> 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
>> 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)
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
> on how to choose
> among the options available in limma for backgroundCorrect that implement 2.
> (i.e., half, minimum, edwards or normexp)?
>> > 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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