[BioC] merging (Combining) microarray datasets on different platforms

[LiGang]

Dear list,

I have one question about merging (Combining) microarray datasets.

I have 50 samples, and each sample was hybridized to 2 different platforms---
GPL3694 (5352 probes) and GPL3696 (also 5352 probes) in duplicate.
There were 168 probes identical between these two platforms. 

I want to merge (combine) two hybridization files of each sample before 
performing normalization for all 50 samples. 
What appropriate method can be used to do this? 
Can the common 168 probes provide some information?

Thanks!
---
LiGang