[BioC] marray and gathering additional information fromGenePixGPR file

[J.delasHeras at ed.ac.uk]

Quoting Marcus Davy <mdavy at hortresearch.co.nz>:

>
> 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.

close to "background", rather.

> 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.

By Abundance you're referring to the A values, right?

What I tend to see is a spread for those spots, it can be quite broad, 
but as you say, they're always distinctly "clustering" at lower A 
values.

If you substract background, then you do get zero values (or 0.5, 
actually, if you use the method "half" to make sure you don't get 
negative intensities, which can happen for those "empty" spots easily)

> They are usually labelled "" or "Empty" in the annotation.

one word of warning: check that empty spots are really empty.

On my latest arrays, I noticed quite a few spots labelled as empty, 
when I could clearly see a spot. I got worried I was using the wrong 
annotation, so I contacted the people who made the arrays. It turned 
out that after printing, they found that they couldn't trust the 
identity of some cDNAs, and they simply marked those spots as "empty" 
in the annotation. It can be very bad, if you're using those spots to 
get an estimate of background, as some people do.

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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