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
