[BioC] Agilent 4x44 single color expression arrays

[Ido M. Tamir]

Dear list,

is there anybody with experience in normalising Agilent
4x44 single color expression arrays?

Any suggestions on preferred normalization methods,
or at least reading it into limma in a way that I can
separate the 4 different conditions (time course) that
are on each array?
I have three biological replicates split on 3 arrays and
each array contains 4 time points.

Maybe I should just pipe it through VSN, but with
Affymetrix I was quite happy with GCRMA and would
actually like to apply a probe model based normalization
method.

thank you very much for your suggestions,
ido