[BioC] single-channel GenePix data

[Sean Davis]

On 6/20/06 8:18 AM, "Svetlana Bulashevska"
<s.bulashevska at dkfz-heidelberg.de> wrote:

> Dear colleagues,
> I have single-channel GenePix data, I have managed to read it in with
> the package limma,
> which is designed for two-color data.
> Could you please give me a tip what can I do further to normalize the data
> and to find differentially expressed genes?
> Thank you very much for the help,

Svetlana,

The major difference between one- and two-channel data is at the
normalization stage.  For one-channel data, there typically needs to be a
"between array" normalization, rather than a "within array" normalization.
Limma offers some between array normalization methods, but you could also
look at some of the methods in the affy packages.  Quantile normalization is
one that has gotten a fair amount of good press and use.  There are others,
though.  You will probably need to evaluate them in your own context before
you can make a decision.

Sean