[BioC] MM > PM intensities

[Lana Schaffer]

Hi,
I have been trying to reproduce the results from the Naef and Magnasco (2003) paper where 95%
of the MM>PM intensities held a purine at the 13th residue.  Using bioconductor, two CEL files from 
the hgu133a chip contained 71% and 72% purines where MM>PM.  A CEL file from the hgu95av2
chip contained 48% purines where MM>PM, but perhaps I need to override the i2xy() function in case
there still exists an error.
Have you found the same discrepancy?  Do you know why my data is not corresponding to the data
in Naef and Magnasco (2003)?

This is my R code:
pmIndexes <- unlist(indexProbes(abatch,"pm"))
mmIndexes <- unlist(indexProbes(abatch,"mm"))
L <- length(pmIndexes)
B13 <- "N"
for (i in 1:L)
{
pm<- intensity(abatch)[pmIndexes[i],]
mm <- intensity(abatch)[mmIndexes[i],]
if (mm > pm) {
probeSequence <- unlist(strsplit(hgu133aprobe[i,]$sequence,""))
B13 <- c(B13,probeSequence[13])
}
}
Thank you for your consideration.
Lana
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