[BioC] Agilent 4x44 single color expression arrays

[Ido M. Tamir]

On Thursday 04 October 2007 06:13, Ido M. Tamir wrote:
> 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
Sorry to follow up on my own e-mail,
but reading it in was simpler than thought after searching
the list archive more carefully.

Now the question remains, which normalization method
people with experience would suggest for expression
arrays or should I use the "gProcessedSignal" column
and be happy?

thank you very much,
ido