[BioC] CDF files

[S Peri]

Hi, 
 I am also trying to parse CDF files to get the
coordinates of the porbesets and their names. The
reason I need to get is that, I want a reference for
each probeset on the chip in this case postion on the
chip. This allows my to query specifically some
probesets depending on the position.  I know this
might sound too much, however, I am interested in
implementing this in the db schema I have.  

I tried Laurent's suggestions. It worked for one
probeset. Is there any command where I get an object
with all probesetIDs and their coordinates written
adjascent to probeset coordinats. 

Thanks.
Peri.


--- Laurent Gautier <lgautier at altern.org> wrote:

> Srinivas Iyyer wrote:
> > Hi, 
> > 
> > CellHeader=X	Y	MEAN	STDV	NPIXELS
> >   0	  0	152.0	30.0	 25
> >   1	  0	5024.5	475.3	 20
> >   2	  0	151.0	25.0	 25
> >   3	  0	5017.0	558.9	 25
> >   4	  0	205.5	71.5	 20
> > 
> > 
> > 
> > 
> > 
> > How can I get to know what 0 0 , 1 0, 2 0
> correspond
> > to 1001_at or XXXX_at.  Can some one please help.
> I
> > want to get the spot and the corresponding probe. 
> 
> The information is contained in the relevant CDF
> file.
> 
> Did you consider using the 'affy' package ?
> 
> The help page for the function 'xy2indices' might be
> worth a look.
> 
> However, if you want to go from XY coordinates to
> probe set names often 
> in your code, the most efficient
> would be to use the class Cdf (now found in the
> package 'makecdfenv').
> 
> 
> L.
> 
> 
> > Thank you.
> > 
> > Srini
> > 
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