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

[J.delasHeras at ed.ac.uk]

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

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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