[BioC] converting Affy indices to x,y coordinates

[Todd Allen]

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