[BioC] microarray: dealing with multi probes for one gene

[Christophe Boutte]

Dear Bioconductors users,

I make a post doc in the oceanic research station of Roscoff (France).

I use the limma bioconductor for analysing microarray results.
There is on my microarrays three replicates for each spot (thus I use 
correlation or average to deal with these values).
My problem is that we have several probes for each gene on the 
microarray: we designed 1 to 5 different probes for each gene, and I do 
not know how to use them:
Should I average them ? It's difficult because the number of probes vary 
depending of each gene (1-5) and I cannot precise the number of "dups". 
I can also use correlation, but I have the same problem of variable 
number of probes.
Has somebody already dealt with this type of problem of variable 
multi-probes by gene ?

thank you in advance,

Christophe Boutte