[BioC] how to get affy probe set physical location on the chip?

[Hassane, Duane]

Hi Yanqin,

Regarding getting physical locations for each probe of the probeset, you can try something like:

indices<-indexProbes(affyBatch,"pm",probeset.id)

where probeset.id is a vector of probeset IDs to get indices corresponding to your probesets of interest.
This returns a named list, named according a probeset id.

locations<-indices2xy(unlist(indices),abatch=affyBatch)

This gives a set of x and y coordinates for each probe of each probeset you specified in probeset.id

That should work.

Hope that helps,

Duane Hassane


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Yanqin Yang
Sent: Thursday, August 03, 2006 12:02 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] how to get affy probe set physical location on the chip?


Hello,
   
  I have a set of rat affymetrix array. One of chip shows there is bright 'blue' corner in the 'sign.resids' image after applied 'affyPLM' package. How could I retrieve the affy ID corresponding the 'blue' area? Or, if I have a set of affy IDs, how could I get their physical location on the array? 
   
  Thanks a lot!
   
  Yanqin

 		
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