On Nov 29, 2007 9:26 AM, Erika <yeh.erika@gmail.com> wrote:

> Dear Wolfgang,
>
> My apologies, I'll try to make my question more precise. I've got a table
> with intensity raw data and flag data obtained from 14 codelink arrays,
> each
> one from a distinct sample, from two categories. I'd like to know how I
> could normalize this data and find differentiatly expressed genes.
> With affy array data, I used to run rma and mas5, and then run empirical
> bayes to find differentiatly expressed genes.
> I hope I made my point clear.
>

Hi, Erika.  You might want to take a look at:

http://bioconductor.org/packages/2.1/bioc/html/codelink.html

I have not used it, but it might do what you want.  That said, if your data
are single-channel data, there are numerous methods you can use to normalize
them.  You could check in the limma documentation (since it sounds like you
are already using limma) for details.

Sean

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