Tiling array analysis tools

I wonder whether you could give me any advice regarding software that could evaluate (measure) transcription levels detected by tiling arrays for established annotation sets. In other words I'm looking for programs that would do the same thing they do for expression arrays (e.g. GeneChip Affy arrays) but in the tiling context.

You might want first to take a look at:

http://tiling.gersteinlab.org/platformcmp/

and the tool Tilescope as described in this paper:
http://papers.gersteinlab.org/papers/tilescope/