Affy CEL files for Tilescope

I was trying to use the TILESCOPE program for analyzing Arabidopsis tiling array data, but was unsuccessful. First of all, the .CEL files were not uploaded as it always showed that the file extension is incorrect. I was wondering if tilescope does not support .CEL files? But in the sample you have provided, there is an option for the same but that never appears on my computer (I am using a Mac machine). Do you think I should be downloading the program in order to solve it?

Tilescope does support CEL files. It is possible that it doesn't recognize your extension if it is not in all lower case. Since it is a web program, it doesn't matter if you're using a Mac or PC or any other OS as long as you're using a browser.

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/