[BioC] Probe Cell

Park, Richard Richard.Park at joslin.harvard.edu
Wed Nov 12 17:00:57 MET 2003

I've had problems using xy2indices function, but to get a list of all the x and y locations for the hg_u95av2 chip, you can go and download the cdf file from:

(you may need to register for affymetrix's website, which is free)

You can then open up the cdf file in notepad, and look for the individual probe names. 

This is the response I received from affymetrix developer's network: 
>I'm afraid the only way to find this info out is to either part the CDF file or use the  SDK and write a program to get the info. For now, the CDF file is an ASCII text file so you >can open it and search for 100001_at. You will see a section that describes the list of >>cells that are part of that probe set. Use the PBase and TBase values to determine whether >a CEL is a PM (PBase != TBase) or MM (PBase = TBase).

Its tedious, I had to write a java program to parse the file for me. But if you are just looking for individual probes, you should be able to view it in notepad. 

hope this is helpful, 
Richard Park 

-----Original Message-----
From: James MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Wednesday, November 12, 2003 10:28 AM
To: s0uchi02 at louisville.edu; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Probe Cell

I think you are looking for xy2indices.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> s0uchi02 <s0uchi02 at louisville.edu> 11/12/03 09:45AM >>>
Hello.  I am using "affy" to process HG_U95Av2 chip.  I want to know
each spot (probe cell) is aligned on a chip.  When I read in a data
(Data <- ReadAffy( )) and write out to a file, each spot is numbered
from 1 to 
409600.  How can I determine probe cells and their corresponding probe
and probe sets from this file?  Is there a list that corresponds to
these spot 
numbers?  I also would like to find out which probe is aligned on which
cell.  Thank you.

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