[BioC] Question on afy/gcrma probe indexes
Rich Haney
rhaney1 at nc.rr.com
Tue Apr 27 23:39:28 CEST 2004
I am using gcrma with the HG133A dataset. When I ask for the location (
index ) of the first probe I get:
(1.) Probe = 1007_s_at1
Index = 129340 [ The probe is at (x,y) =(467,181) ]
As I understand it, the probe position is found using the affy routine
'xy2i'. There, the logic for finding a position from x and y is 0based for
y and 1based for x. So:
(2.) Index = x + nrows * ( y  1 ) with nrows = 712 and, as above, x=467
and y=181
Index = 467 + 712 * ( 181  1 )
= 128627 ( that is, 712 + 1 less than answer given above, 129340
).
So the question is, in affy, is the Index of probes stored with 1based (
not 0based ) y coordinates, while xy2i assumes 0based coordinates?
Thanks for your help!


Notes:
(a.) I believe that this is why my background adjustment is then not
correct:
bg.adjust.optical < function(abatch,minimum=1,verbose=TRUE){
Index < unlist(indexProbes(abatch,"both"))
if(verbose) cat("Adjusting for optical effect")
for(i in 1:length(abatch)){
if(verbose) cat(".")
exprs(abatch)[Index,i] < exprs(abatch)[Index,i] 
min(exprs(abatch)[Index,i],na.rm=TRUE) + minimum
}
(b.) The probe index is created using the following lines of gcrma:
##put it in an affybatch
tmp < get("xy2i",paste("package:",cdfpackagename,sep=""))
affinity.info < new("AffyBatch",cdfName=cdfname)
pmIndex < unlist(indexProbes(affinity.info,"pm"))
mmIndex < unlist(indexProbes(affinity.info,"mm"))
subIndex < match(tmp(p$x,p$y),pmIndex)
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