[BioC] CDF/Probe/Annotation for GNF1m custom chip

[Cei Abreu-Goodger]

Hello all,

I am trying to use affylmGUI to pre-process data from a GNF1m custom Affy
chip. I'm on MacOSX 10.4.9, R 2.4.1, Bioconductor 1.9.

I downloaded the series CEL file from GEO, and I used
make.cdf.package to produce a CDF environment for this chip. I get a
warning, but I can install the package anyway, so maybe it's working?
Warning message:
incomplete final line found by readLines on
'/Library/Frameworks/R.framework/Versions/2.4/Resources/library/makecdfenv/Code/DESCRIPTION'

But when I try to normalize my CEL files, I get an error stating that the
variable "gngnf1musaprobe" was not found. I imagine that, just as I
created a custom CDF environment, I now need custom probe and maybe
annotation objects. Yet I couldn't find something to indicate how to
create these.

The affylmGUI help says to ask this mailing list. Does anyone have any
suggestions?

Thanks,

Cei