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.

Best wishes

Erika

2007/11/28, Wolfgang Huber <huber@ebi.ac.uk>:
>
> Dear Erika,
>
> > I'm a newbie to bioconductor, but I've already done some analysis an
> affy
> > arrays. However, I've got some data obtained in the codelink system that
> I'd
> > like to analyze in bioconductor as well. What packages should I use? Can
> > affy packages be used for these data?
>
> Please have a look at the limma package.
>
> You might also try to formulate your question more precisely. "analyse"
> is a fairly unspecific task description, almost all of the packages on
> Bioconductor can be used for some kind of analysis or other.
>
> Best wishes
>    Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>



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