[BioC] illumina --> limma?

[Sean Davis]

On 8/24/06 2:50 PM, "Anand Patel" <acpatel at gmail.com> wrote:

> Using both mouse and human Sentrix-6 beadarrays, I've managed to
> normalize the arrays both with the beadarray package and the
> BeadExplorer package.  However, despite being able to get an exprSet
> from beadarray and a BeadSummaryList from BeadExplorer, I'm not sure
> how to go to Limma from there.
> 
> The exprSet does contain normalized values for all of the arrays, and
> I can construct a new phenoData, but they're not log-values of
> expression . . .

 newExprSet <- oldExprSet  #copy old exprSet for safe-keeping
 exprs(newExprSet) <- log2(exprs(oldExprSet))   #take log of expression
values

I think that will do it.

Sean