[BioC] Agilent arrays missing spots

[Francois Pepin]

It's indeed a "feature". They have internal controls (or something of the kind) that the scanner is being told to ignore completely.

Go ahead with the NA's, it's the easiest way to deal with it.

Francois

On May 11, 2010, at 8:56 AM, Michael Lawrence wrote:

> On Tue, May 11, 2010 at 6:20 AM, Bjoern Usadel <Usadel at mpimp-golm.mpg.de>wrote:
> 
>> Dear List,
>> 
>> Lately, we are getting some agilent array scans that simply seem to lack
>> some rows meaning that several spots are not available.
>> 
>> Whilst this behaviour is consistent (the same rows i.e. spots are missing
>> across all arrays) it messes up the layout and thus makes an imageplot
>> difficult. So far I have "fixed" this issue by reintroducing dummy lines
>> containing NA data thus restoring the layout.
>> Has anyone else seen this behaviour and maybe found a more insightful
>> solution to this problem or is this maybe even a feature of agilent chips?
>> 
>> 
> I don't know if it is a "feature" but it's the way that many of them are
> designed. Making a rectangle using NA's is the solution that has been
> recommended here in the past. I suggested that the work-around be
> incorporated into arrayQualityMetrics. Not sure if it's been done yet.
> 
> Michael
> 
> 
>> 
>> Best Wishes,
>> Bjoern
>> ---------------------
>> Bjoern Usadel
>> Max Planck Institute of Molecular Plant Physiology
>> Integrative Carbon Biology
>> Am Muehlenberg 1
>> 14476 Potsdam Golm
>> Fon +493315678153
>> Fax +493315678134
>> ---------------------------
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