I would like to use justRMA() in R/bioconductor using a remapped affymetrix CDF for u133a and u133aplus2.0 chips. I'd like to figure out how to ensure that I get an annotated expression set as I would using the affymetrix CDFs.

Do you mean you don't want to use the existing Bioconductor packages, you want to build one from your own custom CDF file? If so, then maybe makecdfenv

@unknown: being as precise as possible when formulating the question can only help you getting a precise answer. Now that is appears clear that you are after alternative mapping, what is exactly "just can't seem to get them to work" ?

I think that [?] is asking about remapping probes for the regular HG-U133A and HG-U133plus2 arrays, not about custom array designs.

ya examples being affyprobeminer or brainarray provided CDFs. i just can't seem to get them to work.

@unknown: being as precise as possible when formulating the question can only help you getting a precise answer. Now that is appears clear that you are after alternative mapping, what is exactly "just can't seem to get them to work" ?