[BioC] (x,y) coordinates and probe intensity

[Ashley Lin]

Dear group,

I know this issue has been discussed before, but I had a hard time figuring 
out how to associate the intensity of a probe in CEL file with the x, y 
coordinates of the probes in the chip.

For example, in Affymetrix U133A chip, the first probe is:

>probe:HG-U133A_2:1007_s_at:416:177; Interrogation_Position=3330; Antisense;
CACCCAGCTGGTCCTGTGGATGGGA

where 416 is x coordinate and 177 is y coordinate on the chip.

But when I use the following command,

>cel<-ReadAffy() # there is only one CELfile in the folder
>pmindex(cel)[1]

I got the location information of the probe set 1007_s_at :

$"1007_s_at"
[1] 129340 213420 396671  82246 430968 427082 432610  72465 432865  99501
[11] 504952 443862 341432 198778 463575  10989

But none of the following equations that mentioned in the list before can 
fit into these numbers

>(Textual description of makecdfenv): j = x*nrow + y + 1
>(Textual description of affy, p.26): j = x*nrow y + 1 (sic!) j = Probe.Y * 
>nrow + Probe.X + 1 (for the perfect match)
>jmm = Probe.Y * nrow + Probe.X + 2 (for the mismatch)

Does nrow refer to the row number of the batch file? Here 
ncol(intensity(cel))=1, nrow(intensity(cel))=506944

Can anybody tell me how this works please?

Thank you very much,
Ashley

_________________________________________________________________
Don’t just search. Find. Check out the new MSN Search!