[BioC] Bug in probeNames()

[Groot, Philip de]

Hello list,
 
I ran into the following particular problem using the Custom CDF-files from Bioconductor 2.0. Please consider the following code:
 
library(simpleaffy)
x <- ReadAffy(cdfname="mm430mmentrezg")
require(sprintf("%sprobe", cleancdfname(cdfName(x), addcdf=F)), character.only=T)
ProbeNames_CustomCDF <- as.character(as.data.frame(mm430mmentrezgprobe)[,4])
 
grep("66736_at", ProbeNames_CustomCDF, fixed=T)
173151 173152 173153 173154 173155 173156 173157
 
However, when I do it the following way different indices are returned:
 
grep("66736_at", probeNames(x), fixed=T)
172057 172058 172059 172060 172061 172062 172063
 
I do not understand the reason for this! To get the order of the basepairs (for this particular probe) I need to use the upper grep-command (I extract the basepairs from the probes library), but to get the CORRECT pm() and mm() intensities I need to use the lower grep-command. Why is this? For the Affymetrix annotation libraries everything works fine (as I would expect).
 
Regards,
 
Dr Philip de Groot
Wageningen University