[BioC] marray and gathering additional information fromGenePixGPR file

Jenny Drnevich drnevich at uiuc.edu
Wed Jul 19 23:29:14 CEST 2006

Hi Marcus,

In my attempt to clarify things, I had a brain lapse and messed it up 
further! Thanks for pointing it out. I meant to say exactly what you said - 
the M values (log2(R/G) or log2(R) - log2(G) ) should be 0 for empty spots. 
It's the absolute ratio R/G that should be 1.


At 06:24 PM 7/18/2006, Marcus Davy wrote:

>Just to add further comment to this discussion about empty spots in GenePix.
>Empty spots could be due to the physical printing not taking place at that
>spot position or buffer which contains no physical cDNA/oligo probe could be
>deposited by the printing quill at that spot position.
>In gpr files I've looked at, GenePix image analysis provides a non zero
>value (but close to zero) to these intensities. On an MA scale, you should
>see them distributed around 0 on the M scale and have Abundance values
>slightly lower than other non expressing spots.
>They are usually labelled "" or "Empty" in the annotation.
>Agilent intensity files I have looked at don't contain these empty spots.
>On 7/9/06 4:33 AM, "J.delasHeras at ed.ac.uk" <J.delasHeras at ed.ac.uk> wrote:
> > 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!
> >
> > Jose
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu

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