[BioC] Agilent 4x44 single color expression arrays

[Sean Davis]

Ido M. Tamir wrote:
> 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?
>   
You can use the gProcessedSignal column, which will already have a 
background correction step done, but you will still need to do a 
between-array normalization of some kind.  Quantile normalization seems 
to be a reasonable candidate.  However, you will still want to do some 
QC by looking at density plots, pairs plots, etc. to make sure that this 
makes sense for your arrays.

Sean