[BioC] Wells number from .gpr

[Henrik Bengtsson]

Hi,

no, a GenePix Result (GPR) file does not contain any information about
the microtiter plates used for spotting.  I've seen some labs adding
plate information to the GenePix Array List (GAL) file, and then it
was just the plate number (not the plate well coordinate).  Such
details are not required and there is no well defined name for it.  I
think this goes under optional "User Defined" column.  You can read
more about the different GenePix file formats on
http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html.

However, if the array has been spotted in a known order, say, from
left to right top to bottom and you know if a 96 or 384 plate has been
used, you can make an "intelligent guess" from where the spot
originates.  I did some of this a few years ago and the code is in the
aroma package (http://www.braju.com/R/).  A good start would be to
look at the help for PlateGroups and PrintdipGroups (dip not tip) in
that package.  plotPrintdipOrder() and plotPrintorder() are also
useful.

Hope this help you get started

Cheers

Henrik


On 3/17/06, Giulio Di Giovanni <perimessaggini at hotmail.com> wrote:
>
> Sorry for the stupid question, I'm totally a baginner in cDNA data
> Analysis...
> Can I derive  the number of wells in a plate from a .gpr file ?
> I would like to use it for the normalization...
>
> I looked in the web and in the mailing list archives, with no big results...
>
> Thanks a lot
>
> Giulio...
>
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