You can get probe sequences and coordinates (usually) from the Affy website:
You'll want to extract the probe-level summarization and you can then plot intensity as a function of position with your genes of interest.
With respect to the probe-level summarization from the oligo package, the code should look something like this:
library(oligo) celFiles = list.celfiles("/path/to/folder", full.names=T) rawData = read.celfiles(celFiles) probesetData = rma(rawData, target="probeset") probeset.expression = exprs(probesetData) probesets = rownames(probesetData)
However, selecting the optimal genes may be tricky. I've tried using the validated genes from this paper, but they didn't seem to show much of a position degradation effect (in the array data that I have checked so far):