[BioC] retrieve expression of all probes in the probe set

[andrea.grilli at ior.it]

Dear BioC list,
I'm performing an analysis with Gene Chip hgu133a plus 2.0 array in  
two different cell lines. I'm interested in the expression of a  
specific gene and two different probesets match it: despite one is  
saying no difference exists, the other is suggesting a strong  
down-regulation.
Checking where the two probes match, the first is mapping on the 3'  
UTR region of the transcript, instead the second has each one of the  
probes composing the probe set on different exons.

So two questions:
- Could be one probe is more reliable than the other? which one and why?
- Do yuo know if it is possible to recover the expression of each  
probe of the probe set? Different splicing variants for this gene  
exist, so I want to check if the expression of each single exon can  
tell me more.

Thanks in advance for your help,
Andrea