[BioC] Analysing Illumina v2 and v3 platforms

[Emanuele Marchi]

Dear All,
I would like to choose the proper package to analyse (and possibly 
merge) data from Illumina arrays of different designs.
The probes content of our arrays, Illumina v2 and v3, overlaps of 77%, 
meaning that v3 arrays retains nearly all the probes present in the old 
v2 layout.
I think the best way might be to analyse the datasets separately using a 
non parametric test, like Rank Product or Wilcoxon rank-sum test, and 
then compare the results.

Does anyone have a particular suggestion about it?What package and/or 
strategy to use?

Thanks a lot in advance,

Kind Regards.

Emanuele