[BioC] converting Affy indices to x,y coordinates

[Mounts, William]

Todd,

It would appear that there is an error in affyxparser.  Testing a number
of cdf files, it appears that index = K * y + x.

Bill

-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of Todd Allen
Sent: Monday, February 14, 2011 11:19 AM
To: bioconductor at r-project.org
Subject: [BioC] converting Affy indices to x,y coordinates

Hello all,

   I have been reading the documentation portion of a package called
"affyxparser."  In the documentation there is a description of the
formulas needed to seemlessly convert between Affymetrix probe indices
and the cooresponding (x,y) coordinate of individual probes.

Copying from the package documentation, the following information is
most relevant:

1. index = K * y + x + 1; where K is the number of columns on the chip
2. y = floor ((index - 1)/K) 3. x=(index - 1) - K * y

In my own work, I am processing a HGU133Plus 2 CDF file. The array
dimensions are (1164, 1164) and if I take the index of a specific probe
listed as 1354890, I calculate the coordinates as x = 1157 and y = 1163
using the formulas above.

The (x,y) coordinate reported from Affy's own CDF file for this probe is
actually x = 1158 (not 1157) and y = 1163.

I am struggling to understand this discrepancy between the affyparser
documentation and the verbatim output from Affy's own CDF file.  Has any
run into this situation before?  Do you see any obvious problem or
explanation as to what is happening.

Thank you!  
Todd A
genesplicer28 at yahoo.com

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