[BioC] marray and gathering additional information fromGenePixGPR file

Marcus Davy mdavy at hortresearch.co.nz
Wed Jul 19 01:24:02 CEST 2006

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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