[BioC] marray and gathering additional information from GenePix GPR file

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Sat Jul 8 18:33:41 CEST 2006

Quoting Jenny Drnevich <drnevich at uiuc.edu>:

> I also want to clarify (for the record) what I meant about spots with '0'
> values - I was referring to the individual channel intensities, not the log
> ratio. If both channels' intensities were 0, then the log ratio would be
> undefined, but in practical terms, the log ratio should be 1 (not changed)
> for undetectable spots. If you are using log ratios for the statistical
> analysis, you might want to check that your undetectable spots are close to
> 1 after pre-processing, and if they are not, you might consider 
> changing them.
> Jenny

Hi Jenny,

I never heard anybody doing that before... but I guess it makes sense. 
Unless the model applied already takes into account the intensities 
somehow... hmmmm, something to think about.
I suppose that's what spot weights are for :-)

ok, end of pointless rambling...

thanks Jenny for those comments!


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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