[BioC] presence/absence call using oligo array?

[xpeng]

Dear Bioc,

Has someone ever used long oligo arrays to test if genes were expressed or 
not? I have two microarray slides on which oligonucleotides (65mer) for genes 
from a parasite genome were spotted. One gene has one oligo but spotted twice 
on each array. One slide has a RNA sample extracted from infected tissues 
(therefore mixture of both parasite RNAs and RNAs from host tissues) 
co-hybridized with RNAs from uninfected host tissue (no parasite RNAs). 
Another is a biological replicate but with dye-swap. People want to know what 
parasite genes are expressed in the infected tissue. Is it possible to do so? 
Related publications are highly appreciated.

Best,
Xinxia