On Tue, May 11, 2010 at 6:20 AM, Bjoern Usadel <Usadel@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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