[BioC] Question on afy/gcrma probe indexes

Wolfgang Huber w.huber at dkfz-heidelberg.de
Wed Apr 28 23:10:06 CEST 2004

Hi Richard,

can you please provide details? An example for when a call to the these 
functions produces a wrong result? So if you are right, we can repair them?

Note that these functions are really simple - e.g. for a hgu133plus2 
chip, they are

> xy2i
function (x, y)
     y * 1164 + x + 1

> i2xy
function (i)
     r = cbind((i - 1)%%1164, (i - 1)%/%1164)
     colnames(r) = c("x", "y")

Best wishes

Park, Richard wrote:
> Hello, 
> I have tried to access the x and y coordinates using xy2i() and i2xy() functions. I would be very cautious about the values you get from these functions. I tried creating a fake .cel file using these functions and the result was never fully correct. 
> I eventually had to download some library file from the affymetrix site that had a full list of each x and y value for each probe set. I am unsure where these files lie on the affymetrix site, since they have undergone a significant revision of their site. But probably on average those functions gave me 30-40 percent correct x and y positions. The only way I was able to get a functional fake .cel file was to use the x and y positions given out by affymetrix. 
> hth, 
> richard Park 

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