[BioC] Limma: background correction. Use or ignore?

[J.delasHeras at ed.ac.uk]

Quoting Naomi Altman <naomi at stat.psu.edu>:

> We have done up to 4 scans of the same arrays at different
> intensities with little apparent degradation of the signal.  We found
> a setting of the scanner that preserved the full optical range, and
> did not try to combine data across scanner levels, although there is
> some literature on this.
>
> --Naomi

Thanks Naomi.

I came across a PERL script called Masliner. It's described in Dudley 
et al. PNAS(2002) 99:7554-7559.
I haven't tested it in any detail yet (so much to do, so little 
time...) but I had it set to run under Cygwin by our local computer 
guy. I also asked him to write a wrapper so that I only need to input 
my two .gpr files (it's only set for Genepix files) and the program 
will produce a "fake" output .gpr that can be used straight away (the 
PERL script alone forces you do do some manual changes). I mean to 
check it soon.

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
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