[BioC] normalizeByReference package for Affymetrix ChIP-chip data

[JENNIFER JUDY]

Hello.

We are currently trying to apply the normalizeByReference package to Affymetrix ChIP-chip data for human and mouse samples. Specifically, I am looking for advice regarding the background parameters (are control samples sufficient in this case). Additionally, does anyone have advice on how to create a probeAnno object with Affy's bpmap files? 

Any help is much appreciated!
Thanks,
Jen