[BioC] Normalizing together Nimblegen arrays with different designs

[Wlasiuk Battagliotti, Gabriela - (wlasiuk)]

Hello,

I am trying to normalize 2 color-arrays from Nimblegen (2.1 promoter arrays) based on control probes using Limma and Ringo.
Some of these arrays have different designs, so probe position (array position) and the number of 'Random' probes differs slightly from batch to batch.
Is there any function built-in these packages (or somewhere else) to take this information into account so the correct probes are used to anchor the normalization within and between arrays?
Thank you in advance,

Gabriela