[BioC] Normalizing single channels within double channel array data

[Wolfgang Huber]

alison waller wrote:
> Hello,
> 
>  
> 
> I have some double channel array experiments (see targets file below).  For
> some of the arrays I do not expect equal amounts of labeled dye
> (specifically the channels with the 'nothing' cDNA have low intensities.
> Basically I want to normalize between arrays, but only using the channels
> that had 'chlor' treatments hybridized to them.  Is there an easy way to do
> this?

Dear Alison,

not just one but many, the two most obvious perhaps being quantile 
normalisation and 'vsn'. See also the vignette of the vsn package and 
the man page of the vsn2 function.

You will need to construct one big matrix (or ExpressionSet), with 
columns = the 'chlor' channels of all arrays.

  Best wishes
	Wolfgang

EBI Cambridge